An in silico approach to design potential siRNA molecules of SARS-CoV-2 Virus structural genes, a preliminary opinion for COVID-19 inhibition

Abstract

The major public health issue now is severe acute respiratory syndrome coronavirus 2 called SARS-CoV-2 or COVID-19 disease that detected in China at the end of 2019 and caused a large global outbreak, World Health Organization (WHO) have shown that this disease become pandemic, the information's about COVID-19 under update till now and different therapeutic strategies still suggesting, the present study introduced An in silico approach to design potential siRNA molecules of SARS-CoV-2 targeting Virus structural genes, as a preliminary opinion for COVID-19 inhibition. the structural genes included spike protein (S), envelope protein (E), membrane protein (M) and nucleocapsid protein (N).the sequence data of SARS-CoV-2 (MN908947.3) used for siRNA designing by siDIRECT bioinformatics tools, the results show there were 177, 539, 27 and 106 siRNA molecules of N, S, E and M genes respectively, then the choosing of some siRNA molecules Tm, low off-targets effect and mismatches nucleotides resulted 18, 24, 2 and 9 siRNA molecules of N, S, E and M genes respectively, the siRNA for the structural proteins were low Tm, low off-targets effect, targeted more than one region at same gene, and molecule sequence started from 30-100 n downstream gene beginning. Study concluded that the dealing with short genes of SARS-CoV-2 was more benefits for siRNA design and targeted more than one gene at the same time may introduce promising results in vivo experiments.