In-Silico Prediction of Sirna to Silence the Sars-Cov-2 Omicron Variant Specifically Ba.4 and Ba.5: An Alternative to Traditional Therapeutics

21 Pages Posted: 19 Jan 2023

See all articles by Rahatul Islam

Rahatul Islam

West Virginia University

Asif Shahriar

University of Texas Rio Grande Valley (UTRGV) (Formerly University of Texas-Pan American)

Nour Fatema

University of Arkansas

Muhammad Ramiz Uddin

University of Oklahoma

Mrityunjoy Acharjee

Stamford University Bangladesh - Department of Microbiology

Md Mukhlesur Rahman Shepon

Shahjalal University of Science and Technology

Avishek Sarkar

Shahjalal University of Science and Technology

Sohag Ahmed

West Virginia University

Abstract

After the first infection in December 2019, the mutating strains of SARS-CoV2 have already affected a lot of healthy people around the world. But situations have not been as devastating as before the first pandemic of the omicron strains of SARS-CoV2. As of June 2022, two more Omicron offshoots, BA.4 and BA.5, are now proliferating worldwide. Perhaps there are more variants already dormant that require only minor changes to resurrect. So, this study was conducted with a view to halting the infection afterwards. In this study, we looked at spike protein to see if any potential siRNAs could be discovered from it. siRNAs, or small interfering RNAs, are now being used as a potential treatment for various genetic conditions or as antiviral or antibacterial therapeutics. In this study, by approaching several computational assays (e.g., GC content, free energy of binding, free energy of folding, RNA-RNA binding, heat capacity, concentration plot, validation, and finally molecular docking analysis), we concluded that two siRNAs could be effective to silence the spike protein of the omicron variant. So, these siRNAs could be a potential target for therapeutic development against the SARS-CoV2 virus by silencing the spike protein of this virus. We believe our research lays the groundwork for the development of effective therapies at the genome level and might be used to develop chemically produced RNA molecules as an antiviral drug against SARS-CoV2 virus infection.

Note:
Funding Information: No specific grant was received for this study.

Declaration of Interests: The authors declare that they have no competing interests.

Ethics Approval Statement: Not required.

Keywords: SARS-CoV2, siRNA, Spike protein, Small interfering RNA, Molecular docking, in silico analysis

Suggested Citation

Islam, Rahatul and Shahriar, Asif and Fatema, Nour and Uddin, Muhammad Ramiz and Acharjee, Mrityunjoy and Shepon, Md Mukhlesur Rahman and Sarkar, Avishek and Ahmed, Sohag, In-Silico Prediction of Sirna to Silence the Sars-Cov-2 Omicron Variant Specifically Ba.4 and Ba.5: An Alternative to Traditional Therapeutics. Available at SSRN: https://ssrn.com/abstract=4327362 or http://dx.doi.org/10.2139/ssrn.4327362

Rahatul Islam (Contact Author)

West Virginia University ( email )

Asif Shahriar

University of Texas Rio Grande Valley (UTRGV) (Formerly University of Texas-Pan American)

Nour Fatema

University of Arkansas ( email )

Muhammad Ramiz Uddin

University of Oklahoma ( email )

Mrityunjoy Acharjee

Stamford University Bangladesh - Department of Microbiology ( email )

Bangladesh

Md Mukhlesur Rahman Shepon

Shahjalal University of Science and Technology ( email )

Kumargaon
Akhalia
Sylhet, HI 3114
Bangladesh

Avishek Sarkar

Shahjalal University of Science and Technology ( email )

Kumargaon
Akhalia
Sylhet, HI 3114
Bangladesh

Sohag Ahmed

West Virginia University ( email )

PO Box 6025
Morgantown, WV 26506
United States

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