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Whole Genome Sequence Analysis and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein 3 of the SARS-CoV-2 Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties

preprint
revised on 24.04.2020 and posted on 27.04.2020 by Arun Shanker, Divya Bhanu, Anjani Alluri, Samriddhi Gupta

The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Acute Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the SARS-CoV-2 has emerged in China. Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and explore the possible antiviral properties of these protein ligand complexes. In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the SARS-CoV-2 whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible binding with ligands that exhibit antiviral properties. Our results showed that the tertiary structure of the polyprotein isolate SARS-CoV-2_HKU-SZ-001_2020 had 98.94 percent identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors. Our results indicate that a part of the viral genome (residues 3268 -3573 in Frame 2 with 306 amino acids) of the SARS-CoV-2 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947.3) when modelled with template 2a5i of the PDB database had 96 percent 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. Docking profile with 9 different conformations of the ligand with the protein model using Autodock Vina showed an affinity of -7.1 Kcal/mol. This region was conserved in 831 genomes of SARS-CoV-2. The part of the genome (residues 1568-1882 in Frame 2 with 315 amino acids) when modelled with template 3e9s of the PDB database had 82 percent identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication. Docking profile with 9 different conformation of the ligand with the protein model using Autodock Vina showed an affinity of -7.9 Kcal/mol. This region was conserved in 831 genomes of SARS-CoV-2. It is possible that these ligands can be antivirals of SARS-CoV-2.

History

Email Address of Submitting Author

arunshank@gmail.com

Institution

Central Research Institute for Dryland Agriculture

Country

India

ORCID For Submitting Author

0000-0001-5635-878X

Declaration of Conflict of Interest

Disclaimer - The research reported is not endorsed by my organization. My organization is not in anyway concerned with this research.This area of research does not fall under the mandate of my organization, this research was conducted in my own interest and funded personally. Open source bioinformatics resources were used for this research.

Version Notes

This is the ninth version of the MS, docking was done with Autodock Vina and the results of the docking was added in this version. Docking study results were added in the MS in Materials and Methods and Results and Discussion sections. Samriddhi Gupta who did the docking study was added in the author list in this version.

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