Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus
Identifieur interne : 000795 ( 2020/Analysis ); précédent : 000794; suivant : 000796Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus
Auteurs : B. Robson [États-Unis, Royaume-Uni]Source :
- Computers in Biology and Medicine [ 0010-4825 ] ; 2020.
Descripteurs français
- KwdFr :
- Animaux, Biologie informatique, Conception de médicament, Conformation des protéines, Coronavirus (), Glycoprotéine de spicule des coronavirus (), Glycoprotéine de spicule des coronavirus (antagonistes et inhibiteurs), Génome viral, Humains, Infections à coronavirus (), Infections à coronavirus (traitement médicamenteux), Langages de programmation, Logiciel, Modèles moléculaires, Pandémies (), Peptidomimétiques (), Peptidomimétiques (métabolisme), Peptidomimétiques (pharmacologie), Pneumopathie virale (), Pneumopathie virale (traitement médicamenteux), Pénétration virale, Similitude de séquences d'acides aminés, Simulation numérique, Structure secondaire des protéines, Séquence d'acides aminés, Vaccins antiviraux (), Vaccins synthétiques, Épitopes.
- MESH :
- antagonistes et inhibiteurs : Glycoprotéine de spicule des coronavirus.
- métabolisme : Peptidomimétiques.
- pharmacologie : Peptidomimétiques.
- traitement médicamenteux : Infections à coronavirus, Pneumopathie virale.
- Animaux, Biologie informatique, Conception de médicament, Conformation des protéines, Coronavirus, Glycoprotéine de spicule des coronavirus, Génome viral, Humains, Infections à coronavirus, Langages de programmation, Logiciel, Modèles moléculaires, Pandémies, Peptidomimétiques, Pneumopathie virale, Pénétration virale, Similitude de séquences d'acides aminés, Simulation numérique, Structure secondaire des protéines, Séquence d'acides aminés, Vaccins antiviraux, Vaccins synthétiques, Épitopes.
English descriptors
- KwdEn :
- Amino Acid Sequence, Animals, Betacoronavirus (chemistry), Betacoronavirus (drug effects), Betacoronavirus (immunology), Betacoronavirus (physiology), Computational Biology, Computer Simulation, Coronavirus (chemistry), Coronavirus Infections (drug therapy), Coronavirus Infections (prevention & control), Drug Design, Epitopes, Genome, Viral, Humans, Models, Molecular, Pandemics (prevention & control), Peptidomimetics (chemistry), Peptidomimetics (metabolism), Peptidomimetics (pharmacology), Pneumonia, Viral (drug therapy), Pneumonia, Viral (prevention & control), Programming Languages, Protein Conformation, Protein Structure, Secondary, Sequence Homology, Amino Acid, Software, Spike Glycoprotein, Coronavirus (antagonists & inhibitors), Spike Glycoprotein, Coronavirus (chemistry), Vaccines, Synthetic, Viral Vaccines (chemistry), Virus Internalization.
- MESH :
- chemical , antagonists & inhibitors : Spike Glycoprotein, Coronavirus.
- chemical , chemistry : Peptidomimetics, Spike Glycoprotein, Coronavirus, Viral Vaccines.
- chemical , metabolism : Peptidomimetics.
- chemical , pharmacology : Peptidomimetics.
- chemical : Epitopes, Vaccines, Synthetic.
- chemistry : Betacoronavirus, Coronavirus.
- drug effects : Betacoronavirus.
- drug therapy : Coronavirus Infections, Pneumonia, Viral.
- immunology : Betacoronavirus.
- physiology : Betacoronavirus.
- prevention & control : Coronavirus Infections, Pandemics, Pneumonia, Viral.
- Amino Acid Sequence, Animals, Computational Biology, Computer Simulation, Drug Design, Genome, Viral, Humans, Models, Molecular, Programming Languages, Protein Conformation, Protein Structure, Secondary, Sequence Homology, Amino Acid, Software, Virus Internalization.
Abstract
This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic, and to explore some design possibilities. The project was originally directed towards a use case for the Q-UEL language and its implementation in a knowledge management and automated inference system for medicine called the BioIngine, but focus here remains mostly on the virus itself. However, using Q-UEL systems to access relevant and emerging literature, and to interact with standard publically available bioinformatics tools on the Internet, did help quickly identify sequences of amino acids that are well conserved across many coronaviruses including 2019-nCoV. KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry. This sequence motif and surrounding variations formed the basis for proposing a specific synthetic vaccine epitope and peptidomimetic agent. The work can, nonetheless, be described in traditional bioinformatics terms, and readily reproduced by others, albeit with the caveat that new data and research into 2019-nCoV is emerging and evolving at an explosive pace. Preliminary studies using molecular modeling and docking, and in that context the potential value of certain known herbal extracts, are also described.
Url:
DOI: 10.1016/j.compbiomed.2020.103670
PubMed: 32209231
PubMed Central: 7094376
Affiliations:
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PMC:7094376Le document en format XML
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Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus</title><author><name sortKey="Robson, B" sort="Robson, B" uniqKey="Robson B" first="B." last="Robson">B. Robson</name><affiliation wicri:level="2"><nlm:aff id="aff1">Ingine Inc., Cleveland, Ohio, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ingine Inc., Cleveland, Ohio</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">The Dirac Foundation, Oxfordshire, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Dirac Foundation, Oxfordshire</wicri:regionArea><wicri:noRegion>Oxfordshire</wicri:noRegion></affiliation></author></analytic><series><title level="j">Computers in Biology and Medicine</title><idno type="ISSN">0010-4825</idno><idno type="eISSN">1879-0534</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Betacoronavirus (chemistry)</term><term>Betacoronavirus (drug 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(chemistry)</term><term>Vaccines, Synthetic</term><term>Viral Vaccines (chemistry)</term><term>Virus Internalization</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Conception de médicament</term><term>Conformation des protéines</term><term>Coronavirus ()</term><term>Glycoprotéine de spicule des coronavirus ()</term><term>Glycoprotéine de spicule des coronavirus (antagonistes et inhibiteurs)</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus ()</term><term>Infections à coronavirus (traitement médicamenteux)</term><term>Langages de programmation</term><term>Logiciel</term><term>Modèles moléculaires</term><term>Pandémies ()</term><term>Peptidomimétiques ()</term><term>Peptidomimétiques (métabolisme)</term><term>Peptidomimétiques (pharmacologie)</term><term>Pneumopathie virale ()</term><term>Pneumopathie virale (traitement médicamenteux)</term><term>Pénétration virale</term><term>Similitude de séquences d'acides aminés</term><term>Simulation numérique</term><term>Structure secondaire des protéines</term><term>Séquence d'acides aminés</term><term>Vaccins antiviraux ()</term><term>Vaccins synthétiques</term><term>Épitopes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptidomimetics</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Vaccines</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Peptidomimetics</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Peptidomimetics</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Epitopes</term><term>Vaccines, Synthetic</term></keywords><keywords scheme="MESH" qualifier="antagonistes et inhibiteurs" 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programmation</term><term>Logiciel</term><term>Modèles moléculaires</term><term>Pandémies</term><term>Peptidomimétiques</term><term>Pneumopathie virale</term><term>Pénétration virale</term><term>Similitude de séquences d'acides aminés</term><term>Simulation numérique</term><term>Structure secondaire des protéines</term><term>Séquence d'acides aminés</term><term>Vaccins antiviraux</term><term>Vaccins synthétiques</term><term>Épitopes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic, and to explore some design possibilities. The project was originally directed towards a use case for the Q-UEL language and its implementation in a knowledge management and automated inference system for medicine called the BioIngine, but focus here remains mostly on the virus itself. However, using Q-UEL systems to access relevant and emerging literature, and to interact with standard publically available bioinformatics tools on the Internet, did help quickly identify sequences of amino acids that are well conserved across many coronaviruses including 2019-nCoV. KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry. This sequence motif and surrounding variations formed the basis for proposing a specific synthetic vaccine epitope and peptidomimetic agent. The work can, nonetheless, be described in traditional bioinformatics terms, and readily reproduced by others, albeit with the caveat that new data and research into 2019-nCoV is emerging and evolving at an explosive pace. Preliminary studies using molecular modeling and docking, and in that context the potential value of certain known herbal extracts, are also described.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Masters, P S" uniqKey="Masters P">P.S. Masters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robson, B" uniqKey="Robson B">B. Robson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, F" uniqKey="Wu F">F. Wu</name></author><author><name sortKey="Zhao, S" uniqKey="Zhao S">S. Zhao</name></author><author><name sortKey="Yu, B" uniqKey="Yu B">B. Yu</name></author><author><name sortKey="Chen, Y M" uniqKey="Chen Y">Y.-M. Chen</name></author><author><name sortKey="Wang, W" uniqKey="Wang W">W. Wang</name></author><author><name sortKey="Hu, Y" uniqKey="Hu Y">Y. Hu</name></author><author><name sortKey="Song, Z G" uniqKey="Song Z">Z.-G. Song</name></author><author><name sortKey="Tao, Z W" uniqKey="Tao Z">Z.-W. Tao</name></author><author><name sortKey="Tian, J H" uniqKey="Tian J">J.-H. Tian</name></author><author><name sortKey="Pei, Y Y" uniqKey="Pei Y">Y.-Y. Pei</name></author><author><name sortKey="Yuan, M L" uniqKey="Yuan M">M.L. Yuan</name></author><author><name sortKey="Zhang, Y L" uniqKey="Zhang Y">Y.-L. Zhang</name></author><author><name sortKey="Dai, F H" uniqKey="Dai F">F.-H. Dai</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y. Liu</name></author><author><name sortKey="Wang, Q M" uniqKey="Wang Q">Q.-M. Wang</name></author><author><name sortKey="Zheng, J J" uniqKey="Zheng J">J.-J. Zheng</name></author><author><name sortKey="Xu, L" uniqKey="Xu L">L. Xu</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.-Z. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, F" uniqKey="Li F">F. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kam, Y W" uniqKey="Kam Y">Y.W. Kam</name></author><author><name sortKey="Okumura, Y" uniqKey="Okumura Y">Y. Okumura</name></author><author><name sortKey="Kido, H" uniqKey="Kido H">H. Kido</name></author><author><name sortKey="Ng, L F P" uniqKey="Ng L">L.F.P. Ng</name></author><author><name sortKey="Bruzzone, R" uniqKey="Bruzzone R">R. Bruzzone</name></author><author><name sortKey="Altmeyer, R" uniqKey="Altmeyer R">R. 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Dai</name></author><author><name sortKey="Wei, D Q" uniqKey="Wei D">D.-Q. Wei</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Khan, M Y" uniqKey="Khan M">M.Y. Khan</name></author><author><name sortKey="Kumar, V" uniqKey="Kumar V">V. Kumar</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Ohio</li></region></list><tree><country name="États-Unis"><region name="Ohio"><name sortKey="Robson, B" sort="Robson, B" uniqKey="Robson B" first="B." last="Robson">B. Robson</name></region></country><country name="Royaume-Uni"><noRegion><name sortKey="Robson, B" sort="Robson, B" uniqKey="Robson B" first="B." last="Robson">B. Robson</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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