In Silico Prediction and Designing of Potential siRNAs to be used as Antivirals Against SARS-CoV-2
- 12 October 2021
- journal article
- research article
- Published by Bentham Science Publishers Ltd. in Current Pharmaceutical Design
- Vol. 27 (32), 3490-3500
- https://doi.org/10.2174/1381612827999210111194101
Abstract
Background: The unusual pneumonia outbreak that originated in the city of Wuhan, China in December 2019 was found to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. Methods: In this work, we have performed an in silico design and prediction of potential siRNAs based on genetic diversity and recombination patterns, targeting various genes of SARS-CoV-2 for antiviral therapeutics. We performed extensive sequence analysis to analyze the genetic diversity and phylogenetic relationships, and to identify the possible source of virus reservoirs and recombination patterns, and the evolution of the virus as well as we designed the siRNAs which can be used as antivirals against SARS-CoV-2. Results: The sequence analysis and phylogenetic relationships indicated high sequence identity and closed clusters with many types of coronavirus. In our analysis, the full-genome of SARS-CoV-2 showed the highest sequence (nucleotide) identity with SARS-bat-ZC45 (87.7%). The overall sequence identity ranged from 74.3% to 87.7% with selected SARS viruses. The recombination analysis indicated the bat SARS virus is a potential recombinant and serves as a major and minor parent. We have predicted 442 siRNAs and finally selected only 19 functional, and potential siRNAs. Conclusions: The siRNAs were predicted and selected based on their greater potency and specificity. The predicted siRNAs need to be validated experimentally for their effective binding and antiviral activity.Keywords
This publication has 42 references indexed in Scilit:
- RNAi: antiviral therapy against dengue virusAsian Pacific Journal of Tropical Biomedicine, 2013
- RNAi in the regulation of mammalian viral infectionsBMC Biology, 2012
- Evidence for a Common Evolutionary Origin of Coronavirus Spike Protein Receptor-Binding SubunitsJournal of Virology, 2012
- siRNA Design Software for a Target Gene-Specific RNA InterferenceFrontiers in Genetics, 2012
- MicroRNAs and human retrovirusesBiochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2011
- MysiRNA-Designer: A Workflow for Efficient siRNA DesignPLOS ONE, 2011
- siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effectBMC Bioinformatics, 2009
- The role of RNAi and microRNAs in animal virus replication and antiviral immunityJournal of Bone and Joint Surgery, 2009
- Effect of target secondary structure on RNAi efficiencyRNA, 2007
- Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirusNature, 2003