Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide.
Identifieur interne : 002A89 ( PubMed/Curation ); précédent : 002A88; suivant : 002A90Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide.
Auteurs : Qi-Shi Du [République populaire de Chine] ; Shu-Qing Wang ; Yu Zhu ; Dong-Qing Wei ; Hong Guo ; Suzanne Sirois ; Kuo-Chen ChouSource :
- Peptides [ 0196-9781 ] ; 2004.
Descripteurs français
- KwdFr :
- Biologie moléculaire, Conception de médicament, Conformation des protéines, Cysteine endopeptidases (), Cysteine endopeptidases (métabolisme), Cystéine (), Glutamine (), Histidine (), Liaison hydrogène, Modèles moléculaires, Peptides (), Simulation numérique, Sites de fixation, Structure moléculaire, Structure tertiaire des protéines, Syndrome respiratoire aigu sévère (virologie), Séquence d'acides aminés, Sérine (), Théorie quantique, Virus du SRAS (), Virus du SRAS (isolement et purification), Virus du SRAS (métabolisme), Électricité statique.
- MESH :
- isolement et purification : Virus du SRAS.
- métabolisme : Cysteine endopeptidases, Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- Biologie moléculaire, Conception de médicament, Conformation des protéines, Cysteine endopeptidases, Cystéine, Glutamine, Histidine, Liaison hydrogène, Modèles moléculaires, Peptides, Simulation numérique, Sites de fixation, Structure moléculaire, Structure tertiaire des protéines, Séquence d'acides aminés, Sérine, Théorie quantique, Virus du SRAS, Électricité statique.
English descriptors
- KwdEn :
- Amino Acid Sequence, Binding Sites, Computer Simulation, Cysteine (chemistry), Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (metabolism), Drug Design, Glutamine (chemistry), Histidine (chemistry), Hydrogen Bonding, Models, Molecular, Molecular Biology, Molecular Structure, Peptides (chemistry), Protein Conformation, Protein Structure, Tertiary, Quantum Theory, SARS Virus (chemistry), SARS Virus (isolation & purification), SARS Virus (metabolism), Serine (chemistry), Severe Acute Respiratory Syndrome (virology), Static Electricity.
- MESH :
- chemical , chemistry : Cysteine, Cysteine Endopeptidases, Glutamine, Histidine, Peptides, Serine.
- chemical , metabolism : Cysteine Endopeptidases.
- chemistry : SARS Virus.
- isolation & purification : SARS Virus.
- metabolism : SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Amino Acid Sequence, Binding Sites, Computer Simulation, Drug Design, Hydrogen Bonding, Models, Molecular, Molecular Biology, Molecular Structure, Protein Conformation, Protein Structure, Tertiary, Quantum Theory, Static Electricity.
Abstract
The cleavage mechanism of severe acute respiratory syndrome (SARS) coronavirus main proteinase (M(pro) or 3CL(pro)) for the octapeptide AVLQSGFR is studied using molecular mechanics (MM) and quantum mechanics (QM). The catalytic dyad His-41 and Cys-145 in the active pocket between domain I and II seem to polarize the pi-electron density of the peptide bond between Gln and Ser in the octapeptide, leading to an increase of positive charge on C(CO) of Gln and negative charge on N(NH) of Ser. The possibility of enhancing the chemical bond between Gln and Ser based on the "distorted key" theory [Anal. Biochem. 233 (1996) 1] is examined. The scissile peptide bond between Gln and Ser is found to be solidified through "hybrid peptide bond" by changing the carbonyl group CO of Gln to CH(2) or CF(2). This leads to a break of the pi-bond system for the peptide bond, making the octapeptide (AVLQSGFR) a "distorted key" and a potential starting system for the design of anti SARS drugs.
DOI: 10.1016/j.peptides.2004.06.018
PubMed: 15501516
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sort="Wei, Dong Qing" uniqKey="Wei D" first="Dong-Qing" last="Wei">Dong-Qing Wei</name></author><author><name sortKey="Guo, Hong" sort="Guo, Hong" uniqKey="Guo H" first="Hong" last="Guo">Hong Guo</name></author><author><name sortKey="Sirois, Suzanne" sort="Sirois, Suzanne" uniqKey="Sirois S" first="Suzanne" last="Sirois">Suzanne Sirois</name></author><author><name sortKey="Chou, Kuo Chen" sort="Chou, Kuo Chen" uniqKey="Chou K" first="Kuo-Chen" last="Chou">Kuo-Chen Chou</name></author></analytic><series><title level="j">Peptides</title><idno type="ISSN">0196-9781</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Computer Simulation</term><term>Cysteine (chemistry)</term><term>Cysteine Endopeptidases (chemistry)</term><term>Cysteine Endopeptidases (metabolism)</term><term>Drug Design</term><term>Glutamine (chemistry)</term><term>Histidine (chemistry)</term><term>Hydrogen Bonding</term><term>Models, Molecular</term><term>Molecular Biology</term><term>Molecular Structure</term><term>Peptides (chemistry)</term><term>Protein Conformation</term><term>Protein Structure, Tertiary</term><term>Quantum Theory</term><term>SARS Virus (chemistry)</term><term>SARS Virus (isolation & purification)</term><term>SARS Virus (metabolism)</term><term>Serine (chemistry)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Static Electricity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biologie moléculaire</term><term>Conception de médicament</term><term>Conformation des protéines</term><term>Cysteine endopeptidases ()</term><term>Cysteine endopeptidases (métabolisme)</term><term>Cystéine ()</term><term>Glutamine ()</term><term>Histidine ()</term><term>Liaison hydrogène</term><term>Modèles moléculaires</term><term>Peptides ()</term><term>Simulation numérique</term><term>Sites de fixation</term><term>Structure moléculaire</term><term>Structure tertiaire des protéines</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Séquence d'acides aminés</term><term>Sérine ()</term><term>Théorie quantique</term><term>Virus du SRAS ()</term><term>Virus du SRAS (isolement et purification)</term><term>Virus du SRAS (métabolisme)</term><term>Électricité statique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cysteine</term><term>Cysteine Endopeptidases</term><term>Glutamine</term><term>Histidine</term><term>Peptides</term><term>Serine</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cysteine Endopeptidases</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cysteine endopeptidases</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Computer Simulation</term><term>Drug Design</term><term>Hydrogen Bonding</term><term>Models, Molecular</term><term>Molecular Biology</term><term>Molecular Structure</term><term>Protein Conformation</term><term>Protein Structure, Tertiary</term><term>Quantum Theory</term><term>Static Electricity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie moléculaire</term><term>Conception de médicament</term><term>Conformation des protéines</term><term>Cysteine endopeptidases</term><term>Cystéine</term><term>Glutamine</term><term>Histidine</term><term>Liaison hydrogène</term><term>Modèles moléculaires</term><term>Peptides</term><term>Simulation numérique</term><term>Sites de fixation</term><term>Structure moléculaire</term><term>Structure tertiaire des protéines</term><term>Séquence d'acides aminés</term><term>Sérine</term><term>Théorie quantique</term><term>Virus du SRAS</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The cleavage mechanism of severe acute respiratory syndrome (SARS) coronavirus main proteinase (M(pro) or 3CL(pro)) for the octapeptide AVLQSGFR is studied using molecular mechanics (MM) and quantum mechanics (QM). The catalytic dyad His-41 and Cys-145 in the active pocket between domain I and II seem to polarize the pi-electron density of the peptide bond between Gln and Ser in the octapeptide, leading to an increase of positive charge on C(CO) of Gln and negative charge on N(NH) of Ser. The possibility of enhancing the chemical bond between Gln and Ser based on the "distorted key" theory [Anal. Biochem. 233 (1996) 1] is examined. The scissile peptide bond between Gln and Ser is found to be solidified through "hybrid peptide bond" by changing the carbonyl group CO of Gln to CH(2) or CF(2). This leads to a break of the pi-bond system for the peptide bond, making the octapeptide (AVLQSGFR) a "distorted key" and a potential starting system for the design of anti SARS drugs.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15501516</PMID><DateCompleted><Year>2005</Year><Month>04</Month><Day>21</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>07</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0196-9781</ISSN><JournalIssue CitedMedium="Print"><Volume>25</Volume><Issue>11</Issue><PubDate><Year>2004</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Peptides</Title><ISOAbbreviation>Peptides</ISOAbbreviation></Journal><ArticleTitle>Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide.</ArticleTitle><Pagination><MedlinePgn>1857-64</MedlinePgn></Pagination><Abstract><AbstractText>The cleavage mechanism of severe acute respiratory syndrome (SARS) coronavirus main proteinase (M(pro) or 3CL(pro)) for the octapeptide AVLQSGFR is studied using molecular mechanics (MM) and quantum mechanics (QM). The catalytic dyad His-41 and Cys-145 in the active pocket between domain I and II seem to polarize the pi-electron density of the peptide bond between Gln and Ser in the octapeptide, leading to an increase of positive charge on C(CO) of Gln and negative charge on N(NH) of Ser. The possibility of enhancing the chemical bond between Gln and Ser based on the "distorted key" theory [Anal. Biochem. 233 (1996) 1] is examined. The scissile peptide bond between Gln and Ser is found to be solidified through "hybrid peptide bond" by changing the carbonyl group CO of Gln to CH(2) or CF(2). This leads to a break of the pi-bond system for the peptide bond, making the octapeptide (AVLQSGFR) a "distorted key" and a potential starting system for the design of anti SARS drugs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Qi-Shi</ForeName><Initials>QS</Initials><AffiliationInfo><Affiliation>Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery, Tianjin 300074, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Shu-Qing</ForeName><Initials>SQ</Initials></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Yu</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Dong-Qing</ForeName><Initials>DQ</Initials></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Hong</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Sirois</LastName><ForeName>Suzanne</ForeName><Initials>S</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>United States</Country><MedlineTA>Peptides</MedlineTA><NlmUniqueID>8008690</NlmUniqueID><ISSNLinking>0196-9781</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010455">Peptides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0RH81L854J</RegistryNumber><NameOfSubstance UI="D005973">Glutamine</NameOfSubstance></Chemical><Chemical><RegistryNumber>452VLY9402</RegistryNumber><NameOfSubstance 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HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:15501516" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |