Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease.
Identifieur interne : 001623 ( Ncbi/Merge ); précédent : 001622; suivant : 001624Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease.
Auteurs : I-Lin Lu [République populaire de Chine] ; Neeraj Mahindroo ; Po-Huang Liang ; Yi-Hui Peng ; Chih-Jung Kuo ; Keng-Chang Tsai ; Hsing-Pang Hsieh ; Yu-Sheng Chao ; Su-Ying WuSource :
- Journal of medicinal chemistry [ 0022-2623 ] ; 2006.
Descripteurs français
- KwdFr :
- Bases de données factuelles, Conception de médicament, Conformation des protéines (), Cristallographie aux rayons X, Cysteine endopeptidases (isolement et purification), Imidazoles (), Imidazoles (pharmacologie), Imidazoles (synthèse chimique), Inhibiteurs de protéases (), Inhibiteurs de protéases (pharmacologie), Inhibiteurs de protéases (synthèse chimique), Liaison hydrogène (), Modèles moléculaires, Oxadiazoles (), Oxadiazoles (pharmacologie), Oxadiazoles (synthèse chimique), Protéines virales (antagonistes et inhibiteurs), Protéines virales (isolement et purification), Pyridines (), Pyridines (pharmacologie), Pyridines (synthèse chimique), Relation structure-activité, Simulation numérique, Sites de fixation, Structure moléculaire, Structure tertiaire des protéines, Sulfones (), Sulfones (pharmacologie), Sulfones (synthèse chimique), Virus du SRAS (enzymologie).
- MESH :
- antagonistes et inhibiteurs : Protéines virales.
- enzymologie : Virus du SRAS.
- isolement et purification : Cysteine endopeptidases, Protéines virales.
- pharmacologie : Imidazoles, Inhibiteurs de protéases, Oxadiazoles, Pyridines, Sulfones.
- synthèse chimique : Imidazoles, Inhibiteurs de protéases, Oxadiazoles, Pyridines, Sulfones.
- Bases de données factuelles, Conception de médicament, Conformation des protéines, Cristallographie aux rayons X, Imidazoles, Inhibiteurs de protéases, Liaison hydrogène, Modèles moléculaires, Oxadiazoles, Pyridines, Relation structure-activité, Simulation numérique, Sites de fixation, Structure moléculaire, Structure tertiaire des protéines, Sulfones.
English descriptors
- KwdEn :
- Binding Sites, Computer Simulation, Crystallography, X-Ray, Cysteine Endopeptidases (isolation & purification), Databases, Factual, Drug Design, Hydrogen Bonding (drug effects), Imidazoles (chemical synthesis), Imidazoles (chemistry), Imidazoles (pharmacology), Models, Molecular, Molecular Structure, Oxadiazoles (chemical synthesis), Oxadiazoles (chemistry), Oxadiazoles (pharmacology), Protease Inhibitors (chemical synthesis), Protease Inhibitors (chemistry), Protease Inhibitors (pharmacology), Protein Conformation (drug effects), Protein Structure, Tertiary, Pyridines (chemical synthesis), Pyridines (chemistry), Pyridines (pharmacology), SARS Virus (enzymology), Structure-Activity Relationship, Sulfones (chemical synthesis), Sulfones (chemistry), Sulfones (pharmacology), Viral Proteins (antagonists & inhibitors), Viral Proteins (isolation & purification).
- MESH :
- chemical , antagonists & inhibitors : Viral Proteins.
- chemical , chemical synthesis : Imidazoles, Oxadiazoles, Protease Inhibitors, Pyridines, Sulfones.
- chemical , chemistry : Imidazoles, Oxadiazoles, Protease Inhibitors, Pyridines, Sulfones.
- chemical , isolation & purification : Cysteine Endopeptidases, Viral Proteins.
- drug effects : Hydrogen Bonding, Protein Conformation.
- enzymology : SARS Virus.
- chemical , pharmacology : Imidazoles, Oxadiazoles, Protease Inhibitors, Pyridines, Sulfones.
- Binding Sites, Computer Simulation, Crystallography, X-Ray, Databases, Factual, Drug Design, Models, Molecular, Molecular Structure, Protein Structure, Tertiary, Structure-Activity Relationship.
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The structure-based virtual screening of a chemical database containing 58,855 compounds followed by the testing of potential compounds for SARS-CoV M(pro) inhibition leads to two hit compounds. The core structures of these two hits, defined by the docking study, are used for further analogue search. Twenty-one analogues derived from these two hits exhibited IC50 values below 50 microM, with the most potent one showing 0.3 microM. Furthermore, the complex structures of two potent inhibitors with SARS-CoV M(pro) were solved by X-ray crystallography. They bind to the protein in a distinct manner compared to all published SARS-CoV M(pro) complex structures. They inhibit SARS-CoV M(pro) activity via intensive H-bond network and hydrophobic interactions, without the formation of a covalent bond. Interestingly, the most potent inhibitor induces protein conformational changes, and the inhibition mechanisms, particularly the disruption of catalytic dyad (His41 and Cys145), are elaborated.
DOI: 10.1021/jm060207o
PubMed: 16913704
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pubmed:16913704Le document en format XML
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synthesis)</term><term>Imidazoles (chemistry)</term><term>Imidazoles (pharmacology)</term><term>Models, Molecular</term><term>Molecular Structure</term><term>Oxadiazoles (chemical synthesis)</term><term>Oxadiazoles (chemistry)</term><term>Oxadiazoles (pharmacology)</term><term>Protease Inhibitors (chemical synthesis)</term><term>Protease Inhibitors (chemistry)</term><term>Protease Inhibitors (pharmacology)</term><term>Protein Conformation (drug effects)</term><term>Protein Structure, Tertiary</term><term>Pyridines (chemical synthesis)</term><term>Pyridines (chemistry)</term><term>Pyridines (pharmacology)</term><term>SARS Virus (enzymology)</term><term>Structure-Activity Relationship</term><term>Sulfones (chemical synthesis)</term><term>Sulfones (chemistry)</term><term>Sulfones (pharmacology)</term><term>Viral Proteins (antagonists & inhibitors)</term><term>Viral Proteins (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données 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moléculaire</term><term>Structure tertiaire des protéines</term><term>Sulfones ()</term><term>Sulfones (pharmacologie)</term><term>Sulfones (synthèse chimique)</term><term>Virus du SRAS (enzymologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemical synthesis" xml:lang="en"><term>Imidazoles</term><term>Oxadiazoles</term><term>Protease Inhibitors</term><term>Pyridines</term><term>Sulfones</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Imidazoles</term><term>Oxadiazoles</term><term>Protease Inhibitors</term><term>Pyridines</term><term>Sulfones</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="antagonistes et 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qualifier="synthèse chimique" xml:lang="fr"><term>Imidazoles</term><term>Inhibiteurs de protéases</term><term>Oxadiazoles</term><term>Pyridines</term><term>Sulfones</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>Crystallography, X-Ray</term><term>Databases, Factual</term><term>Drug Design</term><term>Models, Molecular</term><term>Molecular Structure</term><term>Protein Structure, Tertiary</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données factuelles</term><term>Conception de médicament</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Imidazoles</term><term>Inhibiteurs de protéases</term><term>Liaison hydrogène</term><term>Modèles moléculaires</term><term>Oxadiazoles</term><term>Pyridines</term><term>Relation structure-activité</term><term>Simulation numérique</term><term>Sites de fixation</term><term>Structure moléculaire</term><term>Structure tertiaire des protéines</term><term>Sulfones</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The structure-based virtual screening of a chemical database containing 58,855 compounds followed by the testing of potential compounds for SARS-CoV M(pro) inhibition leads to two hit compounds. The core structures of these two hits, defined by the docking study, are used for further analogue search. Twenty-one analogues derived from these two hits exhibited IC50 values below 50 microM, with the most potent one showing 0.3 microM. Furthermore, the complex structures of two potent inhibitors with SARS-CoV M(pro) were solved by X-ray crystallography. They bind to the protein in a distinct manner compared to all published SARS-CoV M(pro) complex structures. They inhibit SARS-CoV M(pro) activity via intensive H-bond network and hydrophobic interactions, without the formation of a covalent bond. Interestingly, the most potent inhibitor induces protein conformational changes, and the inhibition mechanisms, particularly the disruption of catalytic dyad (His41 and Cys145), are elaborated.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16913704</PMID><DateCompleted><Year>2006</Year><Month>10</Month><Day>03</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0022-2623</ISSN><JournalIssue CitedMedium="Print"><Volume>49</Volume><Issue>17</Issue><PubDate><Year>2006</Year><Month>Aug</Month><Day>24</Day></PubDate></JournalIssue><Title>Journal of medicinal chemistry</Title><ISOAbbreviation>J. Med. Chem.</ISOAbbreviation></Journal><ArticleTitle>Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease.</ArticleTitle><Pagination><MedlinePgn>5154-61</MedlinePgn></Pagination><Abstract><AbstractText>Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The structure-based virtual screening of a chemical database containing 58,855 compounds followed by the testing of potential compounds for SARS-CoV M(pro) inhibition leads to two hit compounds. The core structures of these two hits, defined by the docking study, are used for further analogue search. Twenty-one analogues derived from these two hits exhibited IC50 values below 50 microM, with the most potent one showing 0.3 microM. Furthermore, the complex structures of two potent inhibitors with SARS-CoV M(pro) were solved by X-ray crystallography. They bind to the protein in a distinct manner compared to all published SARS-CoV M(pro) complex structures. They inhibit SARS-CoV M(pro) activity via intensive H-bond network and hydrophobic interactions, without the formation of a covalent bond. Interestingly, the most potent inhibitor induces protein conformational changes, and the inhibition mechanisms, particularly the disruption of catalytic dyad (His41 and Cys145), are elaborated.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>I-Lin</ForeName><Initials>IL</Initials><AffiliationInfo><Affiliation>Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mahindroo</LastName><ForeName>Neeraj</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Po-Huang</ForeName><Initials>PH</Initials></Author><Author ValidYN="Y"><LastName>Peng</LastName><ForeName>Yi-Hui</ForeName><Initials>YH</Initials></Author><Author ValidYN="Y"><LastName>Kuo</LastName><ForeName>Chih-Jung</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Tsai</LastName><ForeName>Keng-Chang</ForeName><Initials>KC</Initials></Author><Author ValidYN="Y"><LastName>Hsieh</LastName><ForeName>Hsing-Pang</ForeName><Initials>HP</Initials></Author><Author ValidYN="Y"><LastName>Chao</LastName><ForeName>Yu-Sheng</ForeName><Initials>YS</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Su-Ying</ForeName><Initials>SY</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>J Med Chem</MedlineTA><NlmUniqueID>9716531</NlmUniqueID><ISSNLinking>0022-2623</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C513855">2-(((3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl)methyl)thio)-4,5-dihydro-1H-imidazole</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C513854">6-methoxy-3-nitro-2-(phenylsulfonyl)pyridine</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D007093">Imidazoles</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010069">Oxadiazoles</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011480">Protease Inhibitors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011725">Pyridines</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D013450">Sulfones</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="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="Y">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003546" MajorTopicYN="N">Cysteine Endopeptidases</DescriptorName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016208" MajorTopicYN="N">Databases, Factual</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015195" MajorTopicYN="Y">Drug Design</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007093" MajorTopicYN="N">Imidazoles</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015394" MajorTopicYN="N">Molecular Structure</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010069" MajorTopicYN="N">Oxadiazoles</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011480" MajorTopicYN="N">Protease Inhibitors</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011725" MajorTopicYN="N">Pyridines</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013329" MajorTopicYN="N">Structure-Activity Relationship</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013450" MajorTopicYN="N">Sulfones</DescriptorName><QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000037" MajorTopicYN="Y">antagonists & inhibitors</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>8</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>10</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>8</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16913704</ArticleId><ArticleId IdType="doi">10.1021/jm060207o</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Chao, Yu Sheng" sort="Chao, Yu Sheng" uniqKey="Chao Y" first="Yu-Sheng" last="Chao">Yu-Sheng Chao</name><name sortKey="Hsieh, Hsing Pang" sort="Hsieh, Hsing Pang" uniqKey="Hsieh H" first="Hsing-Pang" last="Hsieh">Hsing-Pang Hsieh</name><name sortKey="Kuo, Chih Jung" sort="Kuo, Chih Jung" uniqKey="Kuo C" first="Chih-Jung" last="Kuo">Chih-Jung Kuo</name><name sortKey="Liang, Po Huang" sort="Liang, Po Huang" uniqKey="Liang P" first="Po-Huang" last="Liang">Po-Huang Liang</name><name sortKey="Mahindroo, Neeraj" sort="Mahindroo, Neeraj" uniqKey="Mahindroo N" first="Neeraj" last="Mahindroo">Neeraj Mahindroo</name><name sortKey="Peng, Yi Hui" sort="Peng, Yi Hui" uniqKey="Peng Y" first="Yi-Hui" last="Peng">Yi-Hui Peng</name><name sortKey="Tsai, Keng Chang" sort="Tsai, Keng Chang" uniqKey="Tsai K" first="Keng-Chang" last="Tsai">Keng-Chang Tsai</name><name sortKey="Wu, Su Ying" sort="Wu, Su Ying" uniqKey="Wu S" first="Su-Ying" last="Wu">Su-Ying Wu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Lu, I Lin" sort="Lu, I Lin" uniqKey="Lu I" first="I-Lin" last="Lu">I-Lin Lu</name></noRegion></country></tree></affiliations></record>Pour 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