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 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.
['Robson|B|B|']
D000595:Amino Acid Sequence D000818:Animals D000073640:Betacoronavirus D000086382:COVID-19 D000086663:COVID-19 Vaccines D019295:Computational Biology D003198:Computer Simulation D017934:Coronavirus D018352:Coronavirus Infections D015195:Drug Design D000939:Epitopes D016679:Genome, Viral D006801:Humans D008958:Models, Molecular D058873:Pandemics D057786:Peptidomimetics D011024:Pneumonia, Viral D011381:Programming Languages D011487:Protein Conformation D017433:Protein Structure, Secondary D000086402:SARS-CoV-2 D017386:Sequence Homology, Amino Acid D012984:Software D064370:Spike Glycoprotein, Coronavirus D014614:Vaccines, Synthetic D014765:Viral Vaccines D053586:Virus Internalization
Bioinformatics Synthetic vaccine Peptidomimetic Q-UEL language 2019-nCoV coronavirus Automatic browser Retroinverso Wuhan seafood market coronavirus