Analysis of whole genome sequences and homology modelling of a 3C like peptidase and a non-structural protein of the novel coronavirus COVID-19 shows protein ligand interaction with an Aza-peptide and a noncovalent lead inhibitor with possible antiviral properties

The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the Novel COVID-19 has emerged in China Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development Homol modeling of these proteins with known templates offers the opportunity to discover ligand binding sites and possible antiviral properties of these protein ligand complexes Any information emerging from these protein models can be used for vaccine development In this study we did a complete bioinformatic anal , sequence alignment, comparison of multiple sequences and homol modeling of the Novel COVID-19 whole genome sequences, the spike protein and the polyproteins for homol with known proteins, we also analyzed receptor binding sites in these models for possible vaccine development Our results showed that the tertiary structure of the polyprotein isolate COVID-19 _HKU-SZ-001_2020 had 98 94% identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors Our results indicate that a part of the viral genome (residues 254 to 13480 in Frame 2 with 4409 amino acids) of the Novel COVID-19 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947 3) when modeled with template 2a5of the PDdatabase had 96% identity with a 3C like peptidase of SARS-CoV which has ability to bind with Aza-Peptide Epoxide (APE) which is known for irreversible inhibition of SARS-CoV main peptidase The part of the genome when modeled with template 3e9s of the PDdatabase had 82% identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication It is possible that these viral inhibitors can be used for vaccine development for the Novel COVID-19