A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

https://doi.org/10.22146/ijc.68415

Arli Aditya Parikesit(1*), Arif Nur Muhammad Ansori(2), Viol Dhea Kharisma(3)

(1) Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia
(2) Professor Nidom Foundation, Surabaya 60115, Indonesia
(3) Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik 61171, Indonesia
(*) Corresponding Author

Abstract


COVID-19 pandemic has no immediate ending in sight, and any significant increasing cases were observed worldwide. Currently, there are only two main strategies for developing COVID-19 drugs that predominantly use a proteomics-based approach, which are drug repurposing and herbal medicine strategies. However, a third strategy has existed, called small interfering RNA or siRNA, which is based on the transcriptomics approach. In the case of SARS-CoV-2 infection, it is expected to perform by silencing the viral gene, which brings the surface glycoprotein (S) gene responsible for SARS-CoV-2 viral attachment to the ACE2 receptor on the human host cell. This third approach applies a molecular simulation method comprising data retrieval, multiple sequence alignment, phylogenetic tree depiction, 2D/3D structure prediction, and RNA-RNA molecular docking. The expected results are the prediction of 2D and 3D structures of both siRNA and mRNA silenced S genes along with a complex as the result of a docking method formed by those silenced genes. An Insilco chemical interaction study was performed in testing siRNA and mRNA complex’s stability with the confirmation result of a stable complex which is expected to be formed before mRNA reaches the ribosome for the translation process. Thus, siRNA from the S gene could be considered a candidate for the COVID-19 therapeutic agent.

Keywords


COVID-19; SARS-CoV-2; siRNA; S gene; molecular docking

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DOI: https://doi.org/10.22146/ijc.68415

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