Application of bioinformatics in search for cleavable peptides of SARS-CoV M(pro) and chemical modification of octapeptides.
Identifieur interne : 001541 ( Ncbi/Merge ); précédent : 001540; suivant : 001542Application of bioinformatics in search for cleavable peptides of SARS-CoV M(pro) and chemical modification of octapeptides.
Auteurs : Qishi Du [République populaire de Chine] ; Shuqing Wang ; Zhiqin Jiang ; Weina Gao ; Yun Li ; Dongqing Wei ; Kuo-Chen ChouSource :
- Medicinal chemistry (Shariqah (United Arab Emirates)) [ 1573-4064 ] ; 2005.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ARN, Analyse de séquence de protéine, Antiviraux (), Antiviraux (pharmacologie), Biologie informatique, Conception de médicament, Cysteine endopeptidases (), Cysteine endopeptidases (génétique), Données de séquences moléculaires, Génome viral, Inhibiteurs de la cystéine protéinase (), Inhibiteurs de la cystéine protéinase (pharmacologie), Logiciel, Oligopeptides (), Oligopeptides (génétique), Oligopeptides (pharmacologie), Protéines virales (), Protéines virales (antagonistes et inhibiteurs), Protéines virales (génétique), Séquence d'acides aminés, Virus du SRAS (), Virus du SRAS (enzymologie), Virus du SRAS (génétique).
- MESH :
- antagonistes et inhibiteurs : Protéines virales.
- enzymologie : Virus du SRAS.
- génétique : Cysteine endopeptidases, Oligopeptides, Protéines virales, Virus du SRAS.
- pharmacologie : Antiviraux, Inhibiteurs de la cystéine protéinase, Oligopeptides.
- Analyse de séquence d'ARN, Analyse de séquence de protéine, Antiviraux, Biologie informatique, Conception de médicament, Cysteine endopeptidases, Données de séquences moléculaires, Génome viral, Inhibiteurs de la cystéine protéinase, Logiciel, Oligopeptides, Protéines virales, Séquence d'acides aminés, Virus du SRAS.
English descriptors
- KwdEn :
- Amino Acid Sequence, Antiviral Agents (chemistry), Antiviral Agents (pharmacology), Computational Biology, Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (genetics), Cysteine Proteinase Inhibitors (chemistry), Cysteine Proteinase Inhibitors (pharmacology), Drug Design, Genome, Viral, Molecular Sequence Data, Oligopeptides (chemistry), Oligopeptides (genetics), Oligopeptides (pharmacology), SARS Virus (drug effects), SARS Virus (enzymology), SARS Virus (genetics), Sequence Analysis, Protein, Sequence Analysis, RNA, Software, Viral Proteins (antagonists & inhibitors), Viral Proteins (chemistry), Viral Proteins (genetics).
- MESH :
- chemical , antagonists & inhibitors : Viral Proteins.
- chemical , chemistry : Antiviral Agents, Cysteine Endopeptidases, Cysteine Proteinase Inhibitors, Oligopeptides, Viral Proteins.
- chemical , genetics : Cysteine Endopeptidases, Oligopeptides, Viral Proteins.
- chemical , pharmacology : Antiviral Agents, Cysteine Proteinase Inhibitors, Oligopeptides.
- drug effects : SARS Virus.
- enzymology : SARS Virus.
- genetics : SARS Virus.
- Amino Acid Sequence, Computational Biology, Drug Design, Genome, Viral, Molecular Sequence Data, Sequence Analysis, Protein, Sequence Analysis, RNA, Software.
Abstract
According to the "distorted key" theory as elaborated in a review article years ago (Chou, K.C.: Analytical Biochemistry, 1996, 233, 1-14), the knowledge of the cleavable peptides by SARS-CoV M(pro) (severe acute respiratory syndrome coronavirus main proteinase) can provide very useful insights on developing drugs against SARS. In view of this, the softwares, ZCURVE_CoV 1.0 and ZCURVE_CoV 2.0 (http://tubic.tju.edu.cn/sars/), developed recently for SARS-Coronavirus are used to analyze the 36 complete SARS-Coronavirus RNA sequences in the gene bank NCBI (http://www.ncbi.nlm.nih.gov/) from different sources for protein coding genes, and to search for the cleavage sites of SARS-CoV M(pro) in polyproteins pp1a and pp1ab. A total of 396 cleavage points are found in the 36 SARS-Coronavirus and 11 cleavable octapeptides abstracted from the 396 cleavage sites. The statistical distributions of amino acids for the cleavable octapeptides at the subsites R4, R3, R2, R1, R1', R2', R3' and R4' are calculated. The cleavage-specific positions are on R2, R1 and R1', and the positions R3 and R4 are featured by some certain specificity for SARS-CoV M(pro). The structural characters of amino acid residues around the cleavage-specific positions are discussed. Two most promising octapeptides, i.e., NH(2)-ATLQ downward arrowAIAS-COOH and NH(2)-ATLQ downward arrowAENV-COOH, are selected to be the candidates for chemical modification, converting into the inhibitors of SARS-CoV M(pro). A possible strategy to convert a cleavable octapeptide by SARS enzyme into a drug candidate against SARS is elucidated.
DOI: 10.2174/1573406053765468
PubMed: 16787316
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pubmed:16787316Le document en format XML
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(génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Antiviral Agents</term><term>Cysteine Endopeptidases</term><term>Cysteine Proteinase Inhibitors</term><term>Oligopeptides</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Oligopeptides</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term><term>Cysteine Proteinase Inhibitors</term><term>Oligopeptides</term></keywords><keywords scheme="MESH" qualifier="antagonistes et inhibiteurs" xml:lang="fr"><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>SARS Virus</term></keywords><keywords 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d'ARN</term><term>Analyse de séquence de protéine</term><term>Antiviraux</term><term>Biologie informatique</term><term>Conception de médicament</term><term>Cysteine endopeptidases</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Inhibiteurs de la cystéine protéinase</term><term>Logiciel</term><term>Oligopeptides</term><term>Protéines virales</term><term>Séquence d'acides aminés</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">According to the "distorted key" theory as elaborated in a review article years ago (Chou, K.C.: Analytical Biochemistry, 1996, 233, 1-14), the knowledge of the cleavable peptides by SARS-CoV M(pro) (severe acute respiratory syndrome coronavirus main proteinase) can provide very useful insights on developing drugs against SARS. In view of this, the softwares, ZCURVE_CoV 1.0 and ZCURVE_CoV 2.0 (http://tubic.tju.edu.cn/sars/), developed recently for SARS-Coronavirus are used to analyze the 36 complete SARS-Coronavirus RNA sequences in the gene bank NCBI (http://www.ncbi.nlm.nih.gov/) from different sources for protein coding genes, and to search for the cleavage sites of SARS-CoV M(pro) in polyproteins pp1a and pp1ab. A total of 396 cleavage points are found in the 36 SARS-Coronavirus and 11 cleavable octapeptides abstracted from the 396 cleavage sites. The statistical distributions of amino acids for the cleavable octapeptides at the subsites R4, R3, R2, R1, R1', R2', R3' and R4' are calculated. The cleavage-specific positions are on R2, R1 and R1', and the positions R3 and R4 are featured by some certain specificity for SARS-CoV M(pro). The structural characters of amino acid residues around the cleavage-specific positions are discussed. Two most promising octapeptides, i.e., NH(2)-ATLQ downward arrowAIAS-COOH and NH(2)-ATLQ downward arrowAENV-COOH, are selected to be the candidates for chemical modification, converting into the inhibitors of SARS-CoV M(pro). A possible strategy to convert a cleavable octapeptide by SARS enzyme into a drug candidate against SARS is elucidated.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16787316</PMID><DateCompleted><Year>2006</Year><Month>08</Month><Day>28</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1573-4064</ISSN><JournalIssue CitedMedium="Print"><Volume>1</Volume><Issue>3</Issue><PubDate><Year>2005</Year><Month>May</Month></PubDate></JournalIssue><Title>Medicinal chemistry (Shariqah (United Arab Emirates))</Title><ISOAbbreviation>Med Chem</ISOAbbreviation></Journal><ArticleTitle>Application of bioinformatics in search for cleavable peptides of SARS-CoV M(pro) and chemical modification of octapeptides.</ArticleTitle><Pagination><MedlinePgn>209-13</MedlinePgn></Pagination><Abstract><AbstractText>According to the "distorted key" theory as elaborated in a review article years ago (Chou, K.C.: Analytical Biochemistry, 1996, 233, 1-14), the knowledge of the cleavable peptides by SARS-CoV M(pro) (severe acute respiratory syndrome coronavirus main proteinase) can provide very useful insights on developing drugs against SARS. In view of this, the softwares, ZCURVE_CoV 1.0 and ZCURVE_CoV 2.0 (http://tubic.tju.edu.cn/sars/), developed recently for SARS-Coronavirus are used to analyze the 36 complete SARS-Coronavirus RNA sequences in the gene bank NCBI (http://www.ncbi.nlm.nih.gov/) from different sources for protein coding genes, and to search for the cleavage sites of SARS-CoV M(pro) in polyproteins pp1a and pp1ab. A total of 396 cleavage points are found in the 36 SARS-Coronavirus and 11 cleavable octapeptides abstracted from the 396 cleavage sites. The statistical distributions of amino acids for the cleavable octapeptides at the subsites R4, R3, R2, R1, R1', R2', R3' and R4' are calculated. The cleavage-specific positions are on R2, R1 and R1', and the positions R3 and R4 are featured by some certain specificity for SARS-CoV M(pro). The structural characters of amino acid residues around the cleavage-specific positions are discussed. Two most promising octapeptides, i.e., NH(2)-ATLQ downward arrowAIAS-COOH and NH(2)-ATLQ downward arrowAENV-COOH, are selected to be the candidates for chemical modification, converting into the inhibitors of SARS-CoV M(pro). A possible strategy to convert a cleavable octapeptide by SARS enzyme into a drug candidate against SARS is elucidated.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Qishi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Tianjin Normal University, Tianjin Institute of Bioinformatics and Drug Discovery, Tianjin, 300074, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Shuqing</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Zhiqin</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Weina</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yun</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Dongqing</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Chou</LastName><ForeName>Kuo-Chen</ForeName><Initials>KC</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Med Chem</MedlineTA><NlmUniqueID>101240303</NlmUniqueID><ISSNLinking>1573-4064</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000998">Antiviral Agents</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015853">Cysteine Proteinase Inhibitors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009842">Oligopeptides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.22.-</RegistryNumber><NameOfSubstance UI="C099456">3C-like proteinase, Coronavirus</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.22.-</RegistryNumber><NameOfSubstance UI="D003546">Cysteine Endopeptidases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000998" MajorTopicYN="N">Antiviral Agents</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003546" MajorTopicYN="N">Cysteine Endopeptidases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015853" MajorTopicYN="N">Cysteine Proteinase Inhibitors</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015195" MajorTopicYN="Y">Drug Design</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009842" MajorTopicYN="N">Oligopeptides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020539" MajorTopicYN="N">Sequence Analysis, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="N">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000037" MajorTopicYN="Y">antagonists & inhibitors</QualifierName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>6</Month><Day>22</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>8</Month><Day>29</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>6</Month><Day>22</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16787316</ArticleId><ArticleId IdType="doi">10.2174/1573406053765468</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Chou, Kuo Chen" sort="Chou, Kuo Chen" uniqKey="Chou K" first="Kuo-Chen" last="Chou">Kuo-Chen Chou</name><name sortKey="Gao, Weina" sort="Gao, Weina" uniqKey="Gao W" first="Weina" last="Gao">Weina Gao</name><name sortKey="Jiang, Zhiqin" sort="Jiang, Zhiqin" uniqKey="Jiang Z" first="Zhiqin" last="Jiang">Zhiqin Jiang</name><name sortKey="Li, Yun" sort="Li, Yun" uniqKey="Li Y" first="Yun" last="Li">Yun Li</name><name sortKey="Wang, Shuqing" sort="Wang, Shuqing" uniqKey="Wang S" first="Shuqing" last="Wang">Shuqing Wang</name><name sortKey="Wei, Dongqing" sort="Wei, Dongqing" uniqKey="Wei D" first="Dongqing" last="Wei">Dongqing Wei</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Du, Qishi" sort="Du, Qishi" uniqKey="Du Q" first="Qishi" last="Du">Qishi Du</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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