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Coronavirus Nsp2 Protein Homologies to the Bacterial DNA Topoisomerase I and IV Suggest Nsp2 Protein is an Unique RNA Topoisomerase with Novel Target for Drug and Vaccine Development

Asit Kumar Chakraborty

COVID-19 is a deadly infectious (+) stranded RNA Virus which produces a 7098AA length polyprotein that degraded into sixteen polypeptides in infected human cells. As the Coronavirus infections now pandemic claiming >300000 peoples worldwide, discovery of molecular target is great. The biological functions of the Coronavirus non-structural nsp2 protein is unknown. BLAST search is the best method to understand the function of unknown protein on the basis of sequence homology among the known protein amino acid sequence available in the Genbank Database. Few type I DNA topoisomerases show RNA Topoisomerase activity and such activity was found in Nsp2 protein by homology search with Vibrio haemolyticus Type I and type IV DNA topoisomerase as well as E. coli DNA gyrase and DNA primase. The RNA topoisomearse activity of COVID-19 needed to release the RNA-RNA knots and supercoils during (-) strand synthesis followed by sub-genomic mRNA synthesis. Such enzyme would be a target for DNA topoisomerases inhibitors used against bacterial infections and cancer. We concluded that Nsp2 protein is related to Type I and type IVDNA Topoisomerase of Vibrio haemolyticawhere NH2-terminas of topoVI has similarity to CO2H terminas of Nsp2 protein and CO2H domains of topoI has similarity stretches to the NH2-terminus of Nsp2 protein. Deep sea thermophillic bacteria like Desulfococcus sp and Marinobacter sp DNA topoisomerase I have 25%-30% homologies with stretches. Thus, Nsp2 protein is a RNA Topoisomerase of Coronavirus and is a strong candidate for drug design and vaccine development. Thirty amino acids length peptide of Nsp2 protein (H2N-LVN KFL ALC ADSIII GGA KLK ALNLGE TFV-CO2H) may be a good peptide vaccine against Coronavirus. We also designed nsp2F1 primer (5’-CCT GAT AGT CTT GCC GA-3’) and nsp2R1 primer (5’-GAG CAG TTT CAA GAG TGC GG-3’) for RT-PCR based diagnosis of COVID-19 infection. We are first to determine the function of Nsp2 protein of Coronavirus using bioinformatics approach.