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. 2020 Apr;119:103670.
doi: 10.1016/j.compbiomed.2020.103670. Epub 2020 Feb 26.

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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Free PMC article

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

B Robson. Comput Biol Med. .
Free PMC article

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.

Keywords: 2019-nCoV coronavirus; Automatic browser; Bioinformatics; Peptidomimetic; Q-UEL language; Retroinverso; Synthetic vaccine; Wuhan seafood market coronavirus.

Conflict of interest statement

Declaration of competing interest This paper is provided to the community to promote the more general applications of the thinking of Professor Paul A. M. Dirac in human and animal medicine in accordance with the charter of The Dirac Foundation, to emphasize the advantages and simplicity of the basic form of the Hyperbolic Dirac Net, to encourage its use, and to propose at least some of the principles of the associated Q-UEL, a universal exchange language for medicine, as a basis for a standard for interoperability. These mathematical and engineering principles are used, amongst many others in an integrated way, in the algorithms and internal architectural features of the BioIngine.com, a distributed system developed by Ingine Inc. Cleveland, Ohio, for the mining of, and inference from, Very Big Data for commercial purposes.

Figures

Fig. 1
Fig. 1
SARS spike glycoprotein showing approximate position of the two cleavage sites known for that virus. They are assumed to be the same cleavage points with high degree of homology in the Wuhan Seafood Market Coronavirus.
Fig. 2
Fig. 2
The Main Workflow in this Study. The bioinformatics-based approach can also be reproduced by standard tools, but is facilitated by Q-UEL tools, especially with the explosive growth in studies regarding 2019-nCoV.
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Fig. 3
Fig. 3
Emodin, found elsewhere to be an inhibitor of SARS-CoV entry, has some binding features involving the ketone group that are akin to carbenoxelone and to a number of molecules that may be considered as substructures of carbenoxelone's steroid-like ring.

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