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
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 peptidom...
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| description | 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.
•Bioinformatics studies are carried out on the COVID-19 virus.•A sequence motif KRSFIEDLLFNKV is of particular interest.•Based on the above, synthetic peptides are designed.•Preliminary considerations are also given to non-peptide organic molecules. |
| doi_str_mv | 10.1016/j.compbiomed.2020.103670 |
| format | Article |
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•Bioinformatics studies are carried out on the COVID-19 virus.•A sequence motif KRSFIEDLLFNKV is of particular interest.•Based on the above, synthetic peptides are designed.•Preliminary considerations are also given to non-peptide organic molecules.</description><identifier>ISSN: 0010-4825</identifier><identifier>EISSN: 1879-0534</identifier><identifier>DOI: 10.1016/j.compbiomed.2020.103670</identifier><identifier>PMID: 32209231</identifier><language>eng</language><publisher>United States: Elsevier Ltd</publisher><subject>2019-nCoV coronavirus ; Amino Acid Sequence ; Amino acids ; Animals ; Automatic browser ; Betacoronavirus - chemistry ; Betacoronavirus - drug effects ; Betacoronavirus - immunology ; Betacoronavirus - physiology ; Bioinformatics ; Cell activation ; Computational Biology ; Computer Simulation ; Computers ; Coronaviridae ; Coronavirus - chemistry ; Coronavirus Infections - drug therapy ; Coronavirus Infections - prevention & control ; Coronaviruses ; COVID-19 ; COVID-19 Vaccines ; Drug Design ; Epitopes ; Genome, Viral ; Genomes ; Humans ; Knowledge management ; Models, Molecular ; Molecular modelling ; Pandemics - prevention & control ; Peptidomimetic ; Peptidomimetics - chemistry ; Peptidomimetics - metabolism ; Peptidomimetics - pharmacology ; Plant extracts ; Pneumonia, Viral - drug therapy ; Pneumonia, Viral - prevention & control ; Preliminary designs ; Programming Languages ; Protein Conformation ; Protein Structure, Secondary ; Q-UEL language ; Retroinverso ; SARS-CoV-2 ; Seafood ; Sequence Homology, Amino Acid ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Software ; Spike Glycoprotein, Coronavirus - antagonists & inhibitors ; Spike Glycoprotein, Coronavirus - chemistry ; Synthetic vaccine ; Vaccines ; Vaccines, Synthetic ; Viral diseases ; Viral Vaccines - chemistry ; Virus Internalization ; Viruses ; Wuhan seafood market coronavirus</subject><ispartof>Computers in biology and medicine, 2020-04, Vol.119, p.103670-103670, Article 103670</ispartof><rights>2020 Elsevier Ltd</rights><rights>Copyright © 2020 Elsevier Ltd. All rights reserved.</rights><rights>2020. Elsevier Ltd</rights><rights>2020 Elsevier Ltd. All rights reserved. 2020 Elsevier Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c573t-ea6851e2989329a3d66d52dd8aa0e902c2e30d255b7cd207d74fd5802affafa3</citedby><cites>FETCH-LOGICAL-c573t-ea6851e2989329a3d66d52dd8aa0e902c2e30d255b7cd207d74fd5802affafa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0010482520300627$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,776,780,881,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32209231$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Robson, B.</creatorcontrib><title>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</title><title>Computers in biology and medicine</title><addtitle>Comput Biol Med</addtitle><description>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.
•Bioinformatics studies are carried out on the COVID-19 virus.•A sequence motif KRSFIEDLLFNKV is of particular interest.•Based on the above, synthetic peptides are designed.•Preliminary considerations are also given to non-peptide organic molecules.</description><subject>2019-nCoV coronavirus</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Animals</subject><subject>Automatic browser</subject><subject>Betacoronavirus - chemistry</subject><subject>Betacoronavirus - drug effects</subject><subject>Betacoronavirus - immunology</subject><subject>Betacoronavirus - physiology</subject><subject>Bioinformatics</subject><subject>Cell activation</subject><subject>Computational Biology</subject><subject>Computer Simulation</subject><subject>Computers</subject><subject>Coronaviridae</subject><subject>Coronavirus - chemistry</subject><subject>Coronavirus Infections - drug therapy</subject><subject>Coronavirus Infections - prevention & control</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>COVID-19 Vaccines</subject><subject>Drug Design</subject><subject>Epitopes</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Humans</subject><subject>Knowledge management</subject><subject>Models, Molecular</subject><subject>Molecular modelling</subject><subject>Pandemics - prevention & control</subject><subject>Peptidomimetic</subject><subject>Peptidomimetics - chemistry</subject><subject>Peptidomimetics - metabolism</subject><subject>Peptidomimetics - pharmacology</subject><subject>Plant extracts</subject><subject>Pneumonia, Viral - drug therapy</subject><subject>Pneumonia, Viral - prevention & control</subject><subject>Preliminary designs</subject><subject>Programming Languages</subject><subject>Protein Conformation</subject><subject>Protein Structure, Secondary</subject><subject>Q-UEL language</subject><subject>Retroinverso</subject><subject>SARS-CoV-2</subject><subject>Seafood</subject><subject>Sequence Homology, Amino Acid</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Software</subject><subject>Spike Glycoprotein, Coronavirus - antagonists & inhibitors</subject><subject>Spike Glycoprotein, Coronavirus - chemistry</subject><subject>Synthetic vaccine</subject><subject>Vaccines</subject><subject>Vaccines, Synthetic</subject><subject>Viral diseases</subject><subject>Viral Vaccines - chemistry</subject><subject>Virus Internalization</subject><subject>Viruses</subject><subject>Wuhan seafood market coronavirus</subject><issn>0010-4825</issn><issn>1879-0534</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFUstuFDEQHCEQWQK_gCxxCRKztO15XpDC8ooUKYhEuVpeu2fTqx17sGdGyjfyU3izITwunFpuV1d3lSrLGIclB1693S6N74c1-R7tUoDYt2VVw6NswZu6zaGUxeNsAcAhLxpRHmXPYtwCQAESnmZHUghoheSL7McqEU0jhsi0s2ymoHfMUkQdMS7Z14A76snpcMvSOnKdD70eyUQWx8kSRuYdG2-QWYy0ccx3TLN461IrodisjSGHd9yaDQFndGOan5ENOIxkfU_9HVKn_sY7iiPTG00u1T3t5em3y3zlr3PBTgTwNnfp8YatLq7PPuS8fc2MD97pdPcUn2dPOr2L-OK-HmdXnz5erb7k5xefz1an57kpaznmqKum5CjappWi1dJWlS2FtY3WgC0II1CCFWW5ro0VUNu66GzZgNBdpzstj7N3B9phWif_TVKUTFNDoD7ZpLwm9fePoxu18bOqoS1kXSWCk3uC4L9PGEfVUzS422mHfopKyEaWXEpZJOirf6BbPwWX1ClR8Bp4zWFP2BxQJvgYA3YPx3BQ-8CorfodGLUPjDoEJo2-_FPMw-CvhCTA-wMAk6MzYVDREDqDlgKaUVlP_9_yEzVg2iI</recordid><startdate>20200401</startdate><enddate>20200401</enddate><creator>Robson, B.</creator><general>Elsevier Ltd</general><general>Elsevier Limited</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7RV</scope><scope>7X5</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BEZIV</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K6~</scope><scope>K7-</scope><scope>K9.</scope><scope>KB0</scope><scope>LK8</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7P</scope><scope>M7Z</scope><scope>MBDVC</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200401</creationdate><title>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</title><author>Robson, B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c573t-ea6851e2989329a3d66d52dd8aa0e902c2e30d255b7cd207d74fd5802affafa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>2019-nCoV coronavirus</topic><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Animals</topic><topic>Automatic browser</topic><topic>Betacoronavirus - chemistry</topic><topic>Betacoronavirus - drug effects</topic><topic>Betacoronavirus - immunology</topic><topic>Betacoronavirus - physiology</topic><topic>Bioinformatics</topic><topic>Cell activation</topic><topic>Computational Biology</topic><topic>Computer Simulation</topic><topic>Computers</topic><topic>Coronaviridae</topic><topic>Coronavirus - chemistry</topic><topic>Coronavirus Infections - drug therapy</topic><topic>Coronavirus Infections - prevention & control</topic><topic>Coronaviruses</topic><topic>COVID-19</topic><topic>COVID-19 Vaccines</topic><topic>Drug Design</topic><topic>Epitopes</topic><topic>Genome, Viral</topic><topic>Genomes</topic><topic>Humans</topic><topic>Knowledge management</topic><topic>Models, Molecular</topic><topic>Molecular modelling</topic><topic>Pandemics - prevention & control</topic><topic>Peptidomimetic</topic><topic>Peptidomimetics - chemistry</topic><topic>Peptidomimetics - metabolism</topic><topic>Peptidomimetics - pharmacology</topic><topic>Plant extracts</topic><topic>Pneumonia, Viral - drug therapy</topic><topic>Pneumonia, Viral - prevention & control</topic><topic>Preliminary designs</topic><topic>Programming Languages</topic><topic>Protein Conformation</topic><topic>Protein Structure, Secondary</topic><topic>Q-UEL language</topic><topic>Retroinverso</topic><topic>SARS-CoV-2</topic><topic>Seafood</topic><topic>Sequence Homology, Amino Acid</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Software</topic><topic>Spike Glycoprotein, Coronavirus - antagonists & inhibitors</topic><topic>Spike Glycoprotein, Coronavirus - chemistry</topic><topic>Synthetic vaccine</topic><topic>Vaccines</topic><topic>Vaccines, Synthetic</topic><topic>Viral diseases</topic><topic>Viral Vaccines - chemistry</topic><topic>Virus Internalization</topic><topic>Viruses</topic><topic>Wuhan seafood market coronavirus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Robson, B.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nursing & Allied Health Database</collection><collection>Entrepreneurship Database</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Business Premium Collection</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Business Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>ProQuest Biological Science Collection</collection><collection>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Biological Science Database</collection><collection>Biochemistry Abstracts 1</collection><collection>Research Library (Corporate)</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Computers in biology and medicine</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Robson, B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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</atitle><jtitle>Computers in biology and medicine</jtitle><addtitle>Comput Biol Med</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>119</volume><spage>103670</spage><epage>103670</epage><pages>103670-103670</pages><artnum>103670</artnum><issn>0010-4825</issn><eissn>1879-0534</eissn><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.
•Bioinformatics studies are carried out on the COVID-19 virus.•A sequence motif KRSFIEDLLFNKV is of particular interest.•Based on the above, synthetic peptides are designed.•Preliminary considerations are also given to non-peptide organic molecules.</abstract><cop>United States</cop><pub>Elsevier Ltd</pub><pmid>32209231</pmid><doi>10.1016/j.compbiomed.2020.103670</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Computers in biology and medicine, 2020-04, Vol.119, p.103670-103670, Article 103670 |
| issn | 0010-4825 1879-0534 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7094376 |
| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | 2019-nCoV coronavirus Amino Acid Sequence Amino acids Animals Automatic browser Betacoronavirus - chemistry Betacoronavirus - drug effects Betacoronavirus - immunology Betacoronavirus - physiology Bioinformatics Cell activation Computational Biology Computer Simulation Computers Coronaviridae Coronavirus - chemistry Coronavirus Infections - drug therapy Coronavirus Infections - prevention & control Coronaviruses COVID-19 COVID-19 Vaccines Drug Design Epitopes Genome, Viral Genomes Humans Knowledge management Models, Molecular Molecular modelling Pandemics - prevention & control Peptidomimetic Peptidomimetics - chemistry Peptidomimetics - metabolism Peptidomimetics - pharmacology Plant extracts Pneumonia, Viral - drug therapy Pneumonia, Viral - prevention & control Preliminary designs Programming Languages Protein Conformation Protein Structure, Secondary Q-UEL language Retroinverso SARS-CoV-2 Seafood Sequence Homology, Amino Acid Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Software Spike Glycoprotein, Coronavirus - antagonists & inhibitors Spike Glycoprotein, Coronavirus - chemistry Synthetic vaccine Vaccines Vaccines, Synthetic Viral diseases Viral Vaccines - chemistry Virus Internalization Viruses Wuhan seafood market coronavirus |
| title | 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 |
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