Abstract
BackgroundThe 2019-nCoV which is regarded as a novel coronavirus is a positive-sense single-stranded RNA virus. It is infectious to humans and is the cause of the ongoing coronavirus outbreak which has elicited an emergency in public health and a call for immediate international concern has been linked to it. The coronavirus main proteinase which is also known as the 3C-like protease (3CLpro) is a very important protein in all coronaviruses for the role it plays in the replication of the virus and the proteolytic processing of the viral polyproteins. The resultant cytotoxic effect which is a product of consistent viral replication and proteolytic processing of polyproteins can be greatly reduced through the inhibition of the viral main proteinase activities. This makes the 3C-like protease of the coronavirus a potential and promising target for therapeutic agents against the viral infection.ResultsThis study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Comparative physiochemical studies were carried out on the resultant target protein and its template while selected HIV protease inhibitors were docked against the protein binding sites which contained no co-crystallized ligand.ConclusionIn line with results from this study which has shown great consistency with other scientific findings on coronaviruses, we recommend the administration of the selected HIV protease inhibitors as first-line therapeutic agents for the treatment of the current coronavirus epidemic.
Highlights
The 2019-nCoV which is regarded as a novel coronavirus is a positive-sense single-stranded Ribonucleic acid (RNA) virus
Homology modeling which is a computational method for modeling the 3D structure of proteins and regarded as comparative modeling, constructs atomic models based on known structures or structures that have been determined experimentally and likewise share more than 40% sequence homology
As regards the template selection, homologous proteins with determined structures are searched through the Protein Data Bank (PDB) and templates must have alongside a minimum of 40% identity with the target sequence, the highest possible resolution with appropriate cofactors for selection consideration [29]
Summary
The 2019-nCoV which is regarded as a novel coronavirus is a positive-sense single-stranded RNA virus. The coronavirus main proteinase which is known as the 3C-like protease (3CLpro) is a very important protein in all coronaviruses for the role it plays in the replication of the virus and the proteolytic processing of the viral polyproteins. The resultant cytotoxic effect which is a product of consistent viral replication and proteolytic processing of polyproteins can be greatly reduced through the inhibition of the viral main proteinase activities. This makes the 3C-like protease of the coronavirus a potential and promising target for therapeutic agents against the viral infection. The first major step in containing the SARS-CoV-lined infection was to successfully sequence the viral genome, the organization of which was found to exhibit similarity with the genome of other coronaviruses [11]
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