Structural analysis of inhibition mechanisms of aurintricarboxylic acid on SARS-CoV polymerase and other proteins.
Identifieur interne : 000334 ( France/Analysis ); précédent : 000333; suivant : 000335Structural analysis of inhibition mechanisms of aurintricarboxylic acid on SARS-CoV polymerase and other proteins.
Auteurs : Yeeleng Yap [France] ; Xuewu Zhang ; Anton Andonov ; Runtao HeSource :
- Computational biology and chemistry [ 1476-9271 ] ; 2005.
Descripteurs français
- KwdFr :
- Acide aurintricarboxylique (pharmacologie), Alignement de séquences, Antiviraux (pharmacologie), Conformation des protéines, Données de séquences moléculaires, Liaison aux protéines, Modèles moléculaires, Protéines virales (métabolisme), RNA replicase (antagonistes et inhibiteurs), Similitude de séquences d'acides aminés, Séquence d'acides aminés, Virus du SRAS (), Virus du SRAS (métabolisme).
- MESH :
- antagonistes et inhibiteurs : RNA replicase.
- métabolisme : Protéines virales, Virus du SRAS.
- pharmacologie : Acide aurintricarboxylique, Antiviraux.
- Alignement de séquences, Conformation des protéines, Données de séquences moléculaires, Liaison aux protéines, Modèles moléculaires, Similitude de séquences d'acides aminés, Séquence d'acides aminés, Virus du SRAS.
English descriptors
- KwdEn :
- Amino Acid Sequence, Antiviral Agents (pharmacology), Aurintricarboxylic Acid (pharmacology), Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, RNA Replicase (antagonists & inhibitors), SARS Virus (drug effects), SARS Virus (metabolism), Sequence Alignment, Sequence Homology, Amino Acid, Viral Proteins (metabolism).
- MESH :
- chemical , antagonists & inhibitors : RNA Replicase.
- chemical , metabolism : Viral Proteins.
- chemical , pharmacology : Antiviral Agents, Aurintricarboxylic Acid.
- drug effects : SARS Virus.
- metabolism : SARS Virus.
- Amino Acid Sequence, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Sequence Alignment, Sequence Homology, Amino Acid.
Abstract
We recently published experimental results that indicated Aurintricarboxylic Acid (ATA) could selectively inhibit SARS-CoV replication inside host cells by greater than 1000 times. This inhibition suggested that ATA could be developed as potent anti-viral drug. Here, to extend our experimental observation, we have incorporated protein structural studies (with positive/negative controls) to investigate the potential binding modes/sites of ATA onto RNA-dependent RNA polymerase (RdRp) from SARS-CoV and other pathogenic positive-strand RNA-viruses, as well as other proteins in SARS-CoV based on the fact that ATA binds to Ca2+-activated neutral protease (m-calpain), the protein tyrosine phosphatase (PTP) and HIV integrase which have existing crystal structures. Eight regions with homologous 3D-conformation were derived for 10 proteins of interest. One of the region, Rbinding (754-766 in SARS-CoV's RdRp), located in the palm sub-domain mainly constituted of anti-parallel beta-strand-turn-beta-strand hairpin structures that covers two of the three RdRp catalytic sites (Asp 760, Asp761), was also predicted by molecular docking method (based on free energy of binding DeltaG) to be important binding motif recognized by ATA. The existence of this strictly conserved region that incorporated catalytic residues, coupled with the homologous ATA binding pockets and their consistent DeltaG values, suggested strongly ATA may be involved in an analogous inhibition mechanism of SARS-COV's RdRp in concomitant to the case in m-calpain, PTP and HIV integrase.
DOI: 10.1016/j.compbiolchem.2005.04.006
PubMed: 15979041
Affiliations:
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pubmed:15979041Le document en format XML
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Molecular</term><term>Molecular Sequence Data</term><term>Protein Binding</term><term>Protein Conformation</term><term>RNA Replicase (antagonists & inhibitors)</term><term>SARS Virus (drug effects)</term><term>SARS Virus (metabolism)</term><term>Sequence Alignment</term><term>Sequence Homology, Amino Acid</term><term>Viral Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acide aurintricarboxylique (pharmacologie)</term><term>Alignement de séquences</term><term>Antiviraux (pharmacologie)</term><term>Conformation des protéines</term><term>Données de séquences moléculaires</term><term>Liaison aux protéines</term><term>Modèles moléculaires</term><term>Protéines virales (métabolisme)</term><term>RNA replicase (antagonistes et inhibiteurs)</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Virus du SRAS ()</term><term>Virus du SRAS (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>RNA Replicase</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term><term>Aurintricarboxylic Acid</term></keywords><keywords scheme="MESH" qualifier="antagonistes et inhibiteurs" xml:lang="fr"><term>RNA replicase</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines virales</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Acide aurintricarboxylique</term><term>Antiviraux</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Protein Binding</term><term>Protein Conformation</term><term>Sequence Alignment</term><term>Sequence Homology, Amino Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Conformation des protéines</term><term>Données de séquences moléculaires</term><term>Liaison aux protéines</term><term>Modèles moléculaires</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We recently published experimental results that indicated Aurintricarboxylic Acid (ATA) could selectively inhibit SARS-CoV replication inside host cells by greater than 1000 times. This inhibition suggested that ATA could be developed as potent anti-viral drug. Here, to extend our experimental observation, we have incorporated protein structural studies (with positive/negative controls) to investigate the potential binding modes/sites of ATA onto RNA-dependent RNA polymerase (RdRp) from SARS-CoV and other pathogenic positive-strand RNA-viruses, as well as other proteins in SARS-CoV based on the fact that ATA binds to Ca2+-activated neutral protease (m-calpain), the protein tyrosine phosphatase (PTP) and HIV integrase which have existing crystal structures. Eight regions with homologous 3D-conformation were derived for 10 proteins of interest. One of the region, Rbinding (754-766 in SARS-CoV's RdRp), located in the palm sub-domain mainly constituted of anti-parallel beta-strand-turn-beta-strand hairpin structures that covers two of the three RdRp catalytic sites (Asp 760, Asp761), was also predicted by molecular docking method (based on free energy of binding DeltaG) to be important binding motif recognized by ATA. The existence of this strictly conserved region that incorporated catalytic residues, coupled with the homologous ATA binding pockets and their consistent DeltaG values, suggested strongly ATA may be involved in an analogous inhibition mechanism of SARS-COV's RdRp in concomitant to the case in m-calpain, PTP and HIV integrase.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><noCountry><name sortKey="Andonov, Anton" sort="Andonov, Anton" uniqKey="Andonov A" first="Anton" last="Andonov">Anton Andonov</name><name sortKey="He, Runtao" sort="He, Runtao" uniqKey="He R" first="Runtao" last="He">Runtao He</name><name sortKey="Zhang, Xuewu" sort="Zhang, Xuewu" uniqKey="Zhang X" first="Xuewu" last="Zhang">Xuewu Zhang</name></noCountry><country name="France"><region name="Île-de-France"><name sortKey="Yap, Yeeleng" sort="Yap, Yeeleng" uniqKey="Yap Y" first="Yeeleng" last="Yap">Yeeleng Yap</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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