کامپیوتر ها و بیماری های ویروسی. مطالعات اولیه بیوانفورماتیک درباره طراحی واکسن ترکیبی
Abstract
1- Introduction and brief review of coronaviruses and uses of synthetic peptides
2- Theory
3- Methods
4- Results
5- Discussion and conclusions
Declaration of competing interest
References
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.
Introduction and Brief Review of Coronaviruses and Uses of Synthetic Peptides.
Coronaviruses are viruses of both medical and veterinary importance [1]. They include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and the human coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) responsible for the epidemic in 2003, and Middle East respiratory syndrome coronavirus (MERS-CoV). In the past ten years, many new coronaviruses have been identified. They infect a wide range of hosts from mammals to birds and closely related coronaviruses have been identified in distantly related animals suggesting recent interspecies jumps [1]. Like influenza viruses that have similar epidemic properties, they are single stranded RNA viruses with a lipoprotein envelope, and enter the host cells by a Class I fusion protein, i.e. one that does not require any other viral surface proteins for fusion. Viral fusion proteins are potential therapeutic and vaccine targets, and the above is indicative of the possibility that the kind of considerations discussed in the present paper can be extended to broader range of viruses.