Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase
Identifieur interne : 000193 ( Main/Exploration ); précédent : 000192; suivant : 000194Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase
Auteurs : Abdelmonaem Messaoudi [Tunisie] ; Hatem Belguith [Tunisie] ; Jeannette Ben Hamida [Tunisie]Source :
- Theoretical Biology & Medical Modelling [ 1742-4682 ] ; 2013.
Descripteurs français
- KwdFr :
- Antienzymes (composition chimique), Antienzymes (pharmacologie), Données de séquences moléculaires (MeSH), Escherichia coli (effets des médicaments et des substances chimiques), Escherichia coli (enzymologie), Inhibiteurs des bêta-lactamases (MeSH), Modèles théoriques (MeSH), Protéines Escherichia coli (MeSH), Pseudomonas aeruginosa (effets des médicaments et des substances chimiques), Pseudomonas aeruginosa (enzymologie), Similitude de séquences d'acides aminés (MeSH), Séquence d'acides aminés (MeSH), Tests de criblage d'agents antitumoraux (MeSH), bêta-Lactamases (composition chimique).
- MESH :
- composition chimique : Antienzymes, bêta-Lactamases.
- effets des médicaments et des substances chimiques : Escherichia coli, Pseudomonas aeruginosa.
- enzymologie : Escherichia coli, Pseudomonas aeruginosa.
- pharmacologie : Antienzymes.
- Données de séquences moléculaires, Inhibiteurs des bêta-lactamases, Modèles théoriques, Protéines Escherichia coli, Similitude de séquences d'acides aminés, Séquence d'acides aminés, Tests de criblage d'agents antitumoraux.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Drug Screening Assays, Antitumor (MeSH), Enzyme Inhibitors (chemistry), Enzyme Inhibitors (pharmacology), Escherichia coli (drug effects), Escherichia coli (enzymology), Escherichia coli Proteins (MeSH), Models, Theoretical (MeSH), Molecular Sequence Data (MeSH), Pseudomonas aeruginosa (drug effects), Pseudomonas aeruginosa (enzymology), Sequence Homology, Amino Acid (MeSH), beta-Lactamase Inhibitors (MeSH), beta-Lactamases (chemistry).
- MESH :
- chemical , chemistry : Enzyme Inhibitors, beta-Lactamases.
- chemical , pharmacology : Enzyme Inhibitors.
- drug effects : Escherichia coli, Pseudomonas aeruginosa.
- enzymology : Escherichia coli, Pseudomonas aeruginosa.
- Amino Acid Sequence, Drug Screening Assays, Antitumor, Escherichia coli Proteins, Models, Theoretical, Molecular Sequence Data, Sequence Homology, Amino Acid, beta-Lactamase Inhibitors.
Abstract
The SWISS-MODEL tool was utilized to generate three dimensional structures of VEB-1 β-lactamase, and the 3D model VEB-1 was verified using PROCHECK, ERRAT and VERIFY 3D programs. Virtual screening was performed by docking inhibitors obtained from the ZINC Database to the active site of the VEB-1 protein using AutoDock Vina software.
Homology modeling studies were performed to obtain a three-dimensional structure of VEB-1 β-lactamase. The generated model was validated, and virtual screening of a large chemical ligand library with docking simulations was performed using AutoDock software with the ZINC database. On the basis of the dock-score, four molecules were subjected to ADME/TOX analysis, with ZINC4085364 emerging as the most potent inhibitor of the VEB-1 β-lactamase.
Url:
DOI: 10.1186/1742-4682-10-22
PubMed: 23547944
PubMed Central: 3668210
Affiliations:
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Le document en format XML
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1006, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, 09, Rue Docteur Zouheïr Safi - 1006, Tunis</wicri:regionArea></affiliation></author><author><name sortKey="Belguith, Hatem" sort="Belguith, Hatem" uniqKey="Belguith H" first="Hatem" last="Belguith">Hatem Belguith</name><affiliation wicri:level="1"><nlm:aff id="I1">Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, 09, Rue Docteur Zouheïr Safi - 1006, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, 09, Rue Docteur Zouheïr Safi - 1006, Tunis</wicri:regionArea></affiliation></author><author><name sortKey="Ben Hamida, Jeannette" sort="Ben Hamida, Jeannette" uniqKey="Ben Hamida J" first="Jeannette" last="Ben Hamida">Jeannette Ben Hamida</name><affiliation wicri:level="1"><nlm:aff id="I1">Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, 09, Rue Docteur Zouheïr Safi - 1006, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, 09, Rue Docteur Zouheïr Safi - 1006, Tunis</wicri:regionArea></affiliation></author></analytic><series><title level="j">Theoretical Biology & Medical Modelling</title><idno type="eISSN">1742-4682</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Drug Screening Assays, Antitumor (MeSH)</term><term>Enzyme Inhibitors (chemistry)</term><term>Enzyme Inhibitors (pharmacology)</term><term>Escherichia coli (drug effects)</term><term>Escherichia coli (enzymology)</term><term>Escherichia coli Proteins (MeSH)</term><term>Models, Theoretical (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Pseudomonas aeruginosa (drug effects)</term><term>Pseudomonas aeruginosa (enzymology)</term><term>Sequence Homology, Amino Acid (MeSH)</term><term>beta-Lactamase Inhibitors (MeSH)</term><term>beta-Lactamases (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Antienzymes (composition chimique)</term><term>Antienzymes (pharmacologie)</term><term>Données de séquences moléculaires (MeSH)</term><term>Escherichia coli (effets des médicaments et des substances chimiques)</term><term>Escherichia coli (enzymologie)</term><term>Inhibiteurs des bêta-lactamases (MeSH)</term><term>Modèles théoriques (MeSH)</term><term>Protéines Escherichia coli (MeSH)</term><term>Pseudomonas aeruginosa (effets des médicaments et des substances chimiques)</term><term>Pseudomonas aeruginosa (enzymologie)</term><term>Similitude de séquences d'acides aminés (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term><term>Tests de criblage d'agents antitumoraux (MeSH)</term><term>bêta-Lactamases (composition chimique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Enzyme Inhibitors</term><term>beta-Lactamases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Enzyme Inhibitors</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Antienzymes</term><term>bêta-Lactamases</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Escherichia coli</term><term>Pseudomonas aeruginosa</term></keywords><keywords scheme="MESH" qualifier="effets des médicaments et des substances chimiques" xml:lang="fr"><term>Escherichia coli</term><term>Pseudomonas aeruginosa</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Escherichia coli</term><term>Pseudomonas aeruginosa</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Escherichia coli</term><term>Pseudomonas aeruginosa</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antienzymes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Drug Screening Assays, Antitumor</term><term>Escherichia coli Proteins</term><term>Models, Theoretical</term><term>Molecular Sequence Data</term><term>Sequence Homology, Amino Acid</term><term>beta-Lactamase Inhibitors</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Inhibiteurs des bêta-lactamases</term><term>Modèles théoriques</term><term>Protéines Escherichia coli</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Tests de criblage d'agents antitumoraux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p><italic>bla</italic><sub>VEB-1</sub> is an integron-located extended-spectrum β-lactamase gene initially detected in <italic>Escherichia coli</italic> and <italic>Pseudomonas aeruginosa</italic> strains from south-east Asia. Several recent studies have reported that VEB-1-positive strains are highly resistant to ceftazidime, cefotaxime and aztreonam antibiotics. One strategy to overcome resistance involves administering antibiotics together with β-lactamase inhibitors during the treatment of infectious diseases. During this study, four VEB-1 β-lactamase inhibitors were identified using computer-aided drug design.</p></sec><sec><title>Methods</title><p>The SWISS-MODEL tool was utilized to generate three dimensional structures of VEB-1 β-lactamase, and the 3D model VEB-1 was verified using PROCHECK, ERRAT and VERIFY 3D programs. Virtual screening was performed by docking inhibitors obtained from the ZINC Database to the active site of the VEB-1 protein using AutoDock Vina software.</p></sec><sec><title>Results and conclusion</title><p>Homology modeling studies were performed to obtain a three-dimensional structure of VEB-1 β-lactamase. The generated model was validated, and virtual screening of a large chemical ligand library with docking simulations was performed using AutoDock software with the ZINC database. On the basis of the dock-score, four molecules were subjected to ADME/TOX analysis, with ZINC4085364 emerging as the most potent inhibitor of the VEB-1 β-lactamase.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Poirel, L" uniqKey="Poirel L">L Poirel</name></author><author><name sortKey="Naas, T" uniqKey="Naas T">T Naas</name></author><author><name sortKey="Guibert, M" uniqKey="Guibert M">M Guibert</name></author><author><name sortKey="Chaibi, Eb" uniqKey="Chaibi E">EB Chaibi</name></author><author><name sortKey="Labia, R" uniqKey="Labia R">R Labia</name></author><author><name sortKey="Nordmann, P" uniqKey="Nordmann P">P Nordmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Naas, T" uniqKey="Naas T">T Naas</name></author><author><name sortKey="Mikami, Y" uniqKey="Mikami Y">Y Mikami</name></author><author><name sortKey="Imai, T" uniqKey="Imai T">T Imai</name></author><author><name 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Akova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Des Jarlais, Rl" uniqKey="Des Jarlais R">RL Des Jarlais</name></author><author><name sortKey="Seibel, Gl" uniqKey="Seibel G">GL Seibel</name></author><author><name sortKey="Kuntz, Id" uniqKey="Kuntz I">ID Kuntz</name></author><author><name sortKey="Furth, Ps" uniqKey="Furth P">PS Furth</name></author><author><name sortKey="Alvarez, Jc" uniqKey="Alvarez J">JC Alvarez</name></author><author><name sortKey="Ortiz De Montellano, Pr" uniqKey="Ortiz De Montellano P">PR Ortiz De Montellano</name></author><author><name sortKey="De Camp, Dl" uniqKey="De Camp D">DL De Camp</name></author><author><name sortKey="Babe, Lm" uniqKey="Babe L">LM Babé</name></author><author><name sortKey="Craik, Cs" uniqKey="Craik C">CS Craik</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Tunisie</li></country></list><tree><country name="Tunisie"><noRegion><name sortKey="Messaoudi, Abdelmonaem" sort="Messaoudi, Abdelmonaem" uniqKey="Messaoudi A" first="Abdelmonaem" last="Messaoudi">Abdelmonaem Messaoudi</name></noRegion><name sortKey="Belguith, Hatem" sort="Belguith, Hatem" uniqKey="Belguith H" first="Hatem" last="Belguith">Hatem Belguith</name><name sortKey="Ben Hamida, Jeannette" sort="Ben Hamida, Jeannette" uniqKey="Ben Hamida J" first="Jeannette" last="Ben Hamida">Jeannette Ben Hamida</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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