In silico Evaluation of ssDNA Aptamer against 2GHV of SARS-CoV
DOI:
https://doi.org/10.11113/jomalisc.v4.96Keywords:
aptamer, docking, in silico, molecular modelling, SARS-CoVAbstract
SARS is an infectious disease that caused a global outbreak due to the novel coronavirus (SARS-CoV). This disease could cause severe symptoms in humans and even lead to fatality. The screening of SARS can be challenging, whether in terms of cost, time or energy. The goal of this study is to investigate the potential binding of the CoV-RBD-1C aptamer, which was retrieved from a previously reported journal. This aptamer targets 2GHV, the SARS-CoV spike protein receptor binding domain (RBD), obtained from the Protein Data Bank (PBD). Several bioinformatics tools, including Mfold, RNAComposer, and PyMOL, were used to design the predicted aptamer. The structures for both aptamer and target protein were minimized using GROMACS software, and the HDOCK web server was used as a docking tool. The optimization strategy for improving the aptamer’s binding affinity was only conducted with the truncation method. The results indicated that the binding affinity between the optimized aptamer and the target protein is higher compared to the unrefined aptamer. The study also documented the incorporation of the chosen reporter, DAPI, into the designed ssDNA aptamer and then bound it against the target protein. The result showed that the binding affinity of RBC-APT01-DAPI-2GHV was significantly higher than that of RBC-APT-2GHV. The incorporation of ssDNA aptamer-reporter into the target protein suggests that the aptamer may be designed as an aptasensor in the future. This RBC-APT01-DAPI-2GHV also provides an opportunity for creating a new technique for the recognition of SARS-CoV and also helps in the diagnosis of the disease.
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