A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV).
Identifieur interne : 002619 ( Ncbi/Merge ); précédent : 002618; suivant : 002620A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV).
Auteurs : Shengjie Dong [République populaire de Chine] ; Jiachen Sun [République populaire de Chine] ; Zhuo Mao [République populaire de Chine] ; Lu Wang [République populaire de Chine] ; Yi-Lin Lu [République populaire de Chine] ; Jiesen Li [République populaire de Chine]Source :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Abstract
During an outbreak of respiratory diseases including atypical pneumonia in Wuhan, a previously unknown β-coronavirus was detected in patients. The newly discovered coronavirus is similar to some β-coronaviruses found in bats but different from previously known SARS-CoV and MERS-CoV. High sequence identities and similarities between 2019-nCoV and SARS-CoV were found. In this study, we searched the homologous templates of all nonstructural and structural proteins of 2019-nCoV. Among the nonstructural proteins, the leader protein (nsp1), the papain-like protease (nsp3), the nsp4, the 3C-like protease (nsp5), the nsp7, the nsp8, the nsp9, the nsp10, the RNA-directed RNA polymerase (nsp12), the helicase (nsp13), the guanine-N7 methyltransferase (nsp14), the uridylate-specific endoribonuclease (nsp15), the 2'-O-methyltransferase (nsp16), and the ORF7a protein could be built on the basis of homology templates. Among the structural proteins, the spike protein (S-protein), the envelope protein (E-protein), and the nucleocapsid protein (N-protein) can be constructed based on the crystal structures of the proteins from SARS-CoV. It is known that PL-Pro, 3CL-Pro, and RdRp are important targets for design antiviral drugs against 2019-nCoV. And S protein is a critical target candidate for inhibitor screening or vaccine design against 2019-nCoV because coronavirus replication is initiated by the binding of S protein to cell surface receptors. It is believed that these proteins should be useful for further structure-based virtual screening and related computer-aided drug development and vaccine design.
DOI: 10.1002/jmv.25768
PubMed: 32181901
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type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Sun, Jiachen" sort="Sun, Jiachen" uniqKey="Sun J" first="Jiachen" last="Sun">Jiachen Sun</name><affiliation wicri:level="3"><nlm:affiliation>School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Mao, Zhuo" sort="Mao, Zhuo" uniqKey="Mao Z" first="Zhuo" last="Mao">Zhuo Mao</name><affiliation wicri:level="3"><nlm:affiliation>Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, Department of Applied Physics, Institute of Advanced Materials Physics, Faculty of Science, Tianjin University, Tianjin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, Department of Applied Physics, Institute of Advanced Materials Physics, Faculty of Science, Tianjin University, Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Lu" sort="Wang, Lu" uniqKey="Wang L" first="Lu" last="Wang">Lu Wang</name><affiliation wicri:level="1"><nlm:affiliation>School of Science, Inner Mongolia University of Science & Technology, Baotou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Science, Inner Mongolia University of Science & Technology, Baotou</wicri:regionArea><wicri:noRegion>Baotou</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Yi Lin" sort="Lu, Yi Lin" uniqKey="Lu Y" first="Yi-Lin" last="Lu">Yi-Lin Lu</name><affiliation wicri:level="1"><nlm:affiliation>College of New Energy, Bohai University, Jinzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of New Energy, Bohai University, Jinzhou</wicri:regionArea><wicri:noRegion>Jinzhou</wicri:noRegion></affiliation></author><author><name sortKey="Li, Jiesen" sort="Li, Jiesen" uniqKey="Li J" first="Jiesen" last="Li">Jiesen Li</name><affiliation wicri:level="1"><nlm:affiliation>School of Environment and Chemical Engineering, Foshan University, Foshan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Environment and Chemical Engineering, Foshan University, Foshan</wicri:regionArea><wicri:noRegion>Foshan</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of medical virology</title><idno type="eISSN">1096-9071</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">During an outbreak of respiratory diseases including atypical pneumonia in Wuhan, a previously unknown β-coronavirus was detected in patients. The newly discovered coronavirus is similar to some β-coronaviruses found in bats but different from previously known SARS-CoV and MERS-CoV. High sequence identities and similarities between 2019-nCoV and SARS-CoV were found. In this study, we searched the homologous templates of all nonstructural and structural proteins of 2019-nCoV. Among the nonstructural proteins, the leader protein (nsp1), the papain-like protease (nsp3), the nsp4, the 3C-like protease (nsp5), the nsp7, the nsp8, the nsp9, the nsp10, the RNA-directed RNA polymerase (nsp12), the helicase (nsp13), the guanine-N7 methyltransferase (nsp14), the uridylate-specific endoribonuclease (nsp15), the 2'-O-methyltransferase (nsp16), and the ORF7a protein could be built on the basis of homology templates. Among the structural proteins, the spike protein (S-protein), the envelope protein (E-protein), and the nucleocapsid protein (N-protein) can be constructed based on the crystal structures of the proteins from SARS-CoV. It is known that PL-Pro, 3CL-Pro, and RdRp are important targets for design antiviral drugs against 2019-nCoV. And S protein is a critical target candidate for inhibitor screening or vaccine design against 2019-nCoV because coronavirus replication is initiated by the binding of S protein to cell surface receptors. It is believed that these proteins should be useful for further structure-based virtual screening and related computer-aided drug development and vaccine design.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32181901</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>05</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Mar</Month><Day>17</Day></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV).</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25768</ELocationID><Abstract><AbstractText>During an outbreak of respiratory diseases including atypical pneumonia in Wuhan, a previously unknown β-coronavirus was detected in patients. The newly discovered coronavirus is similar to some β-coronaviruses found in bats but different from previously known SARS-CoV and MERS-CoV. High sequence identities and similarities between 2019-nCoV and SARS-CoV were found. In this study, we searched the homologous templates of all nonstructural and structural proteins of 2019-nCoV. Among the nonstructural proteins, the leader protein (nsp1), the papain-like protease (nsp3), the nsp4, the 3C-like protease (nsp5), the nsp7, the nsp8, the nsp9, the nsp10, the RNA-directed RNA polymerase (nsp12), the helicase (nsp13), the guanine-N7 methyltransferase (nsp14), the uridylate-specific endoribonuclease (nsp15), the 2'-O-methyltransferase (nsp16), and the ORF7a protein could be built on the basis of homology templates. Among the structural proteins, the spike protein (S-protein), the envelope protein (E-protein), and the nucleocapsid protein (N-protein) can be constructed based on the crystal structures of the proteins from SARS-CoV. It is known that PL-Pro, 3CL-Pro, and RdRp are important targets for design antiviral drugs against 2019-nCoV. And S protein is a critical target candidate for inhibitor screening or vaccine design against 2019-nCoV because coronavirus replication is initiated by the binding of S protein to cell surface receptors. It is believed that these proteins should be useful for further structure-based virtual screening and related computer-aided drug development and vaccine design.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dong</LastName><ForeName>Shengjie</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Faculty of Education and Sports, Guangdong Baiyun University, Guangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Jiachen</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mao</LastName><ForeName>Zhuo</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, Department of Applied Physics, Institute of Advanced Materials Physics, Faculty of Science, Tianjin University, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Lu</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>School of Science, Inner Mongolia University of Science & Technology, Baotou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Yi-Lin</ForeName><Initials>YL</Initials><AffiliationInfo><Affiliation>College of New Energy, Bohai University, Jinzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jiesen</ForeName><Initials>J</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-5230-2874</Identifier><AffiliationInfo><Affiliation>School of Environment and Chemical Engineering, Foshan University, Foshan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Research and Development, Guangzhou Ginpie Technology Co., Ltd., Guangzhou, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>Gg040934</GrantID><Agency>High-Level Talent Start-Up Research Project of Foshan University</Agency><Country></Country></Grant><Grant><GrantID>2019MS01013</GrantID><Agency>Natural Science Foundation of Inner Mongolia</Agency><Country></Country></Grant><Grant><GrantID>2018015</GrantID><Agency>Opening Project of Guangdong Province Key Laboratory of Computational Science at the Sun Yat-sen University</Agency><Country></Country></Grant><Grant><GrantID>2017QDL-B14</GrantID><Agency>Project of Inner Mongolia University of Science & Technology</Agency><Country></Country></Grant><Grant><GrantID>2017BYKY29</GrantID><Agency>Project of Guangdong Baiyun University</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Med Virol</MedlineTA><NlmUniqueID>7705876</NlmUniqueID><ISSNLinking>0146-6615</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">2019-nCoV</Keyword><Keyword MajorTopicYN="N">BLAST algorithm</Keyword><Keyword MajorTopicYN="N">CLUSTAL analysis</Keyword><Keyword MajorTopicYN="N">MERS-CoV</Keyword><Keyword MajorTopicYN="N">SARS-CoV</Keyword><Keyword MajorTopicYN="N">coronavirus</Keyword><Keyword MajorTopicYN="N">homology modeling</Keyword><Keyword MajorTopicYN="N">sequence alignment</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32181901</ArticleId><ArticleId IdType="doi">10.1002/jmv.25768</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Drosten C, Günther S, Preiser W, et al. 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Nature. 2020;579:270-273. https://doi.org/10.1038/s41586-020-2012-7</Citation></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Guangdong</li></region><settlement><li>Jiangmen</li><li>Tianjin</li></settlement></list><tree><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Dong, Shengjie" sort="Dong, Shengjie" uniqKey="Dong S" first="Shengjie" last="Dong">Shengjie Dong</name></region><name sortKey="Li, Jiesen" sort="Li, Jiesen" uniqKey="Li J" first="Jiesen" last="Li">Jiesen Li</name><name sortKey="Lu, Yi Lin" sort="Lu, Yi Lin" uniqKey="Lu Y" first="Yi-Lin" last="Lu">Yi-Lin Lu</name><name sortKey="Mao, Zhuo" sort="Mao, Zhuo" uniqKey="Mao Z" first="Zhuo" last="Mao">Zhuo Mao</name><name sortKey="Sun, Jiachen" sort="Sun, Jiachen" uniqKey="Sun J" first="Jiachen" last="Sun">Jiachen Sun</name><name sortKey="Wang, Lu" sort="Wang, Lu" uniqKey="Wang L" first="Lu" last="Wang">Lu Wang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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